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  1. Content type: Methodology article

    Understanding the genetic networks and their role in chronic diseases (e.g., cancer) is one of the important objectives of biological researchers. In this work, we present a text mining system that constructs ...

    Authors: Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf and Dirar Homouz

    Citation: BMC Bioinformatics 2019 20:70

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  2. Content type: Research article

    Non-coding RNAs (ncRNAs) are emerging as key regulators and play critical roles in a wide range of tumorigenesis. Recent studies have suggested that long non-coding RNAs (lncRNAs) could interact with microRNAs...

    Authors: Qiu Xiao, Jiawei Luo, Cheng Liang, Jie Cai, Guanghui Li and Buwen Cao

    Citation: BMC Bioinformatics 2019 20:67

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  3. Content type: Research article

    Harmonization techniques make different gene expression profiles and their sets compatible and ready for comparisons. Here we present a new bioinformatic tool termed Shambhala for harmonization of multiple hum...

    Authors: Nicolas Borisov, Irina Shabalina, Victor Tkachev, Maxim Sorokin, Andrew Garazha, Andrey Pulin, Ilya I. Eremin and Anton Buzdin

    Citation: BMC Bioinformatics 2019 20:66

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  4. Content type: Software

    Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In ...

    Authors: Imane Boudellioua, Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos and Robert Hoehndorf

    Citation: BMC Bioinformatics 2019 20:65

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  5. Content type: Research

    The main objectives of this study were sequencing, assembling, and annotation of chloroplast genome of one of the main Siberian boreal forest tree conifer species Siberian larch (Larix sibirica Ledeb.) and detect...

    Authors: Eugeniya I. Bondar, Yuliya A. Putintseva, Nataliya V. Oreshkova and Konstantin V. Krutovsky

    Citation: BMC Bioinformatics 2019 20(Suppl 1):38

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

  6. Content type: Research

    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

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

  7. Content type: Database

    Population structure of fungal infections in wheat differs between wheat varieties and environments. Taking into account evolution of host-pathogen interactions, genetic diversity of both wheat and fungus must...

    Authors: Fedor V. Kazantsev, Ekaterina S. Skolotneva, Vasiliy N. Kelbin, Elena A. Salina and Sergey A. Lashin

    Citation: BMC Bioinformatics 2019 20(Suppl 1):36

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

  8. Content type: Research

    The utilization of high resolution genome data has important implications for the phylogeographical evaluation of non-human species. Biogeographical analyses can yield detailed understanding of their populatio...

    Authors: Ranajit Das and Priyanka Upadhyai

    Citation: BMC Bioinformatics 2019 20(Suppl 1):35

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

  9. Content type: Research

    Consideration of tissue-specific gene expression in reconstruction and analysis of molecular genetic networks is necessary for a proper description of the processes occurring in a specified tissue. Currently, ...

    Authors: Vladimir A. Ivanisenko, Pavel S. Demenkov, Timofey V. Ivanisenko, Elena L. Mishchenko and Olga V. Saik

    Citation: BMC Bioinformatics 2019 20(Suppl 1):34

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

  10. Content type: Research

    In silico prediction of potential drug side-effects is of crucial importance for drug development, since wet experimental identification of drug side-effects is expensive and time-consuming. Existing computationa...

    Authors: Yi Zheng, Hui Peng, Shameek Ghosh, Chaowang Lan and Jinyan Li

    Citation: BMC Bioinformatics 2019 19(Suppl 13):554

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    This article is part of a Supplement: Volume 19 Supplement 13

  11. Content type: Research

    Functional modules in protein-protein interaction networks (PPIN) are defined by maximal sets of functionally associated proteins and are vital to understanding cellular mechanisms and identifying disease asso...

    Authors: Rama Kaalia and Jagath C. Rajapakse

    Citation: BMC Bioinformatics 2019 19(Suppl 13):553

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    This article is part of a Supplement: Volume 19 Supplement 13

  12. Content type: Research

    Among the diverse roles of the Type III secretion-system (T3SS), one of the notable functions is that it serves as unique nano machineries in gram-negative bacteria that facilitate the translocation of effecto...

    Authors: Sapna M. Borah and Anupam Nath Jha

    Citation: BMC Bioinformatics 2019 19(Suppl 13):552

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    This article is part of a Supplement: Volume 19 Supplement 13

  13. Content type: Research

    Small open reading frames (smORF/sORFs) that encode short protein sequences are often overlooked during the standard gene prediction process thus leading to many sORFs being left undiscovered and/or misannotat...

    Authors: Shuhaila Mat-Sharani and Mohd Firdaus-Raih

    Citation: BMC Bioinformatics 2019 19(Suppl 13):551

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    This article is part of a Supplement: Volume 19 Supplement 13

  14. Content type: Software

    Traditional drug discovery approaches are time-consuming, tedious and expensive. Identifying a potential drug-like molecule using high throughput screening (HTS) with high confidence is always a challenging ta...

    Authors: Deepak R. Bharti, Anmol J. Hemrom and Andrew M. Lynn

    Citation: BMC Bioinformatics 2019 19(Suppl 13):550

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    This article is part of a Supplement: Volume 19 Supplement 13

  15. Content type: Research

    Malignant diseases have become a threat for health care system. A panoply of biological processes is involved as the cause of these diseases. In order to unveil the mechanistic details of these diseased states...

    Authors: Sagnik Sen, Ashmita Dey, Sourav Chowdhury, Ujjwal Maulik and Krishnananda Chattopadhyay

    Citation: BMC Bioinformatics 2019 19(Suppl 13):549

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  16. Content type: Research

    Indirect anthropometry (IA) is one of the craniofacial anthropometry methods to perform the measurements on the digital facial images. In order to get the linear measurements, a few definable points on the str...

    Authors: Arpah Abu, Chee Guan Ngo, Nur Idayu Adira Abu-Hassan and Siti Adibah Othman

    Citation: BMC Bioinformatics 2019 19(Suppl 13):548

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  17. Content type: Research

    Glycation is a one of the post-translational modifications (PTM) where sugar molecules and residues in protein sequences are covalently bonded. It has become one of the clinically important PTM in recent times...

    Authors: Hamendra Manhar Reddy, Alok Sharma, Abdollah Dehzangi, Daichi Shigemizu, Abel Avitesh Chandra and Tatushiko Tsunoda

    Citation: BMC Bioinformatics 2019 19(Suppl 13):547

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  18. Content type: Research

    In the current scenario, designing of world-wide effective malaria vaccine against Plasmodium falciparum remain challenging despite the significant progress has been made in last few decades. Conventional vaccino...

    Authors: Manisha Pritam, Garima Singh, Suchit Swaroop, Akhilesh Kumar Singh and Satarudra Prakash Singh

    Citation: BMC Bioinformatics 2019 19(Suppl 13):468

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  19. Content type: Research

    With the recent advancements in high-throughput experimental procedures, biologists are gathering huge quantities of data. A main priority in bioinformatics and computational biology is to provide system level...

    Authors: Wajdi Dhifli, Julia Puig, Aurélien Dispot and Mohamed Elati

    Citation: BMC Bioinformatics 2019 19(Suppl 13):466

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  20. Content type: Research

    Molecular docking studies on protein-peptide interactions are a challenging and time-consuming task because peptides are generally more flexible than proteins and tend to adopt numerous conformations. There ar...

    Authors: Piyush Agrawal, Harinder Singh, Hemant Kumar Srivastava, Sandeep Singh, Gaurav Kishore and Gajendra P. S. Raghava

    Citation: BMC Bioinformatics 2019 19(Suppl 13):426

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  21. Content type: Research

    Advances in medical domain has led to an increase of clinical data production which offers enhancement opportunities for clinical research sector. In this paper, we propose to expand the scope of Electronic Me...

    Authors: Nurul Aqilah Mohd Nor, Nur Aishah Taib, Marniza Saad, Hana Salwani Zaini, Zahir Ahmad, Yamin Ahmad and Sarinder Kaur Dhillon

    Citation: BMC Bioinformatics 2019 19(Suppl 13):402

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  22. Content type: Research

    Although in silico drug discovery is necessary for drug development, two major strategies, a structure-based and ligand-based approach, have not been completely successful. Currently, the third approach, infer...

    Authors: Y-h. Taguchi

    Citation: BMC Bioinformatics 2019 19(Suppl 13):388

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  23. Content type: Software

    DNA methylation is an epigenetic mechanism of genomic regulation involved in the maintenance of homeostatic balance. Dysregulation of DNA methylation status is one of the driver alterations occurring in neopla...

    Authors: Saverio Candido, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Giulia Russo, Giuseppe Sgroi, Valentina Di Salvatore, Massimo Libra and Francesco Pappalardo

    Citation: BMC Bioinformatics 2019 19(Suppl 13):385

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  24. Content type: Research

    Glutarylation, the addition of a glutaryl group (five carbons) to a lysine residue of a protein molecule, is an important post-translational modification and plays a regulatory role in a variety of physiologic...

    Authors: Kai-Yao Huang, Hui-Ju Kao, Justin Bo-Kai Hsu, Shun-Long Weng and Tzong-Yi Lee

    Citation: BMC Bioinformatics 2019 19(Suppl 13):384

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  25. Content type: Research

    Molecular Recognition Features (MoRFs) are short protein regions present in intrinsically disordered protein (IDPs) sequences. MoRFs interact with structured partner protein and upon interaction, they undergo ...

    Authors: Ronesh Sharma, Alok Sharma, Ashwini Patil and Tatsuhiko Tsunoda

    Citation: BMC Bioinformatics 2019 19(Suppl 13):378

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  26. Content type: Research

    Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databa...

    Authors: Duleepa Jayasundara, Damayanthi Herath, Damith Senanayake, Isaam Saeed, Cheng-Yu Yang, Yuan Sun, Bill C. Chang, Sen-Lin Tang and Saman K. Halgamuge

    Citation: BMC Bioinformatics 2019 19(Suppl 13):377

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  27. Content type: Research

    (−)-Balanol is an ATP-mimicking inhibitor that non-selectively targets protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA). While PKA constantly shows tumor promoting activities, PKC isozym...

    Authors: Ari Hardianto, Varun Khanna, Fei Liu and Shoba Ranganathan

    Citation: BMC Bioinformatics 2019 19(Suppl 13):342

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 13

  28. Content type: Software

    Scientific data and research results are being published at an unprecedented rate. Many database curators and researchers utilize data and information from the primary literature to populate databases, form hy...

    Authors: Christian Simon, Kristian Davidsen, Christina Hansen, Emily Seymour, Mike Bogetofte Barnkob and Lars Rønn Olsen

    Citation: BMC Bioinformatics 2019 19(Suppl 13):57

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    This article is part of a Supplement: Volume 19 Supplement 13

  29. Content type: Research article

    Benefiting from big data, powerful computation and new algorithmic techniques, we have been witnessing the renaissance of deep learning, particularly the combination of natural language processing (NLP) and de...

    Authors: Xiaozheng Li, Huazhen Wang, Huixin He, Jixiang Du, Jian Chen and Jinzhun Wu

    Citation: BMC Bioinformatics 2019 20:62

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  30. Content type: Software

    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

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  31. Content type: Software

    High-throughput technologies for analyzing chromosome conformation at a genome scale have revealed that chromatin is organized in topologically associated domains (TADs). While TADs are relatively stable acros...

    Authors: Konstantin Okonechnikov, Serap Erkek, Jan O. Korbel, Stefan M. Pfister and Lukas Chavez

    Citation: BMC Bioinformatics 2019 20:60

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  32. Content type: Software

    Exploring cellular responses to stimuli using extensive gene expression profiles has become a routine procedure performed on a daily basis. Raw and processed data from these studies are available on public dat...

    Authors: Marco Moretto, Paolo Sonego, Ana B. Villaseñor-Altamirano and Kristof Engelen

    Citation: BMC Bioinformatics 2019 20:54

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  33. Content type: Software

    Long reads provide valuable information regarding the sequence composition of genomes. Long reads are usually very noisy which renders their alignments on the reference genome a daunting task. It may take days...

    Authors: Mostafa Hadadian Nejad Yousefi, Maziar Goudarzi and Seyed Abolfazl Motahari

    Citation: BMC Bioinformatics 2019 20:51

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  34. Content type: Software

    The biomedical literature is expanding at ever-increasing rates, and it has become extremely challenging for researchers to keep abreast of new data and discoveries even in their own domains of expertise. We i...

    Authors: Patricia Maraver, Rubén Armañanzas, Todd A. Gillette and Giorgio A. Ascoli

    Citation: BMC Bioinformatics 2019 20:50

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  35. Content type: Software

    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

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  36. Content type: Research article

    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

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  37. Content type: Software

    Samples pooling is a method widely used in studies to reduce costs and labour. DNA sample pooling combined with massive parallel sequencing is a powerful tool for discovering DNA variants (polymorphisms) in la...

    Authors: Aleksandr Igorevich Zhernakov, Alexey Mikhailovich Afonin, Natalia Dmitrievna Gavriliuk, Olga Mikhailovna Moiseeva and Vladimir Aleksandrovich Zhukov

    Citation: BMC Bioinformatics 2019 20:45

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