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  1. Content type: Software

    Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to...

    Authors: Taewoon Joo, Ji-Hye Choi, Ji-Hye Lee, So Eun Park, Youngsic Jeon, Sae Hoon Jung and Hyun Goo Woo

    Citation: BMC Bioinformatics 2019 20:90

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  2. Content type: Research article

    The investigation of intracellular metabolism is the mainstay in the biotechnology and physiology settings. Intracellular metabolic rates are commonly evaluated using labeling pattern of the identified metabol...

    Authors: Di Du, Lin Tan, Yumeng Wang, Bo Peng, John N. Weinstein, Fredric E. Wondisford, Xiaoyang Su and Philip L. Lorenzi

    Citation: BMC Bioinformatics 2019 20:89

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  3. Content type: Software

    High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) has become a routine tool for biodiversity survey and ecological studies. By including sample-specific tags in the primers prior PC...

    Authors: Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski and Tristan Cordier

    Citation: BMC Bioinformatics 2019 20:88

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  4. Content type: Research article

    Long non-coding RNAs play an important role in human complex diseases. Identification of lncRNA-disease associations will gain insight into disease-related lncRNAs and benefit disease diagnoses and treatment. ...

    Authors: Xiao-Nan Fan, Shao-Wu Zhang, Song-Yao Zhang, Kunju Zhu and Songjian Lu

    Citation: BMC Bioinformatics 2019 20:87

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  5. Content type: Research article

    The identification of prognostic genes that can distinguish the prognostic risks of cancer patients remains a significant challenge. Previous works have proven that functional gene sets were more reliable for ...

    Authors: Xiong-Hui Zhou, Xin-Yi Chu, Gang Xue, Jiang-Hui Xiong and Hong-Yu Zhang

    Citation: BMC Bioinformatics 2019 20:85

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  6. Content type: Software

    Prioritisation of gene ontology terms from differential gene expression analyses in a two-dimensional format remains a challenge with exponentially growing data volumes. Typically, gene ontology terms are repr...

    Authors: Irina Kuznetsova, Artur Lugmayr, Stefan J. Siira, Oliver Rackham and Aleksandra Filipovska

    Citation: BMC Bioinformatics 2019 20:84

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  7. Content type: Methodology article

    Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but requi...

    Authors: Arnaud Amzallag, Sridhar Ramaswamy and Cyril H. Benes

    Citation: BMC Bioinformatics 2019 20:83

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  8. Content type: Software

    Life science research is moving quickly towards large-scale experimental designs that are comprised of multiple tissues, time points, and samples. Omic time-series experiments offer answers to three big questi...

    Authors: Joshua R. Williams, Ruoting Yang, John L. Clifford, Daniel Watson, Ross Campbell, Derese Getnet, Raina Kumar, Rasha Hammamieh and Marti Jett

    Citation: BMC Bioinformatics 2019 20:81

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  9. Content type: Methodology article

    Cell counting from cell cultures is required in multiple biological and biomedical research applications. Especially, accurate brightfield-based cell counting methods are needed for cell growth analysis. With ...

    Authors: Kaisa Liimatainen, Lauri Kananen, Leena Latonen and Pekka Ruusuvuori

    Citation: BMC Bioinformatics 2019 20:80

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  10. Content type: Software

    Functional annotation of genes is an essential step in omics data analysis. Multiple databases and methods are currently available to summarize the functions of sets of genes into higher level representations,...

    Authors: Giovanni Scala, Angela Serra, Veer Singh Marwah, Laura Aliisa Saarimäki and Dario Greco

    Citation: BMC Bioinformatics 2019 20:79

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  11. Content type: Software

    With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software ...

    Authors: Yongzhi Yang, Ying Li, Qiao Chen, Yongshuai Sun and Zhiqiang Lu

    Citation: BMC Bioinformatics 2019 20:75

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  12. Content type: Methodology article

    Biomarker discovery studies have been moving the focus from a single target gene to a set of target genes. However, the number of target genes in a drug should be minimum to avoid drug side-effect or toxicity....

    Authors: Sunjoo Bang, Sangjoon Son, Sooyoung Kim and Hyunjung Shin

    Citation: BMC Bioinformatics 2019 20:74

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  13. Content type: Software

    Reconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative and -positive interactions make this progress even more complicated. Al...

    Authors: Minoo Ashtiani, Payman Nickchi, Soheil Jahangiri-Tazehkand, Abdollah Safari, Mehdi Mirzaie and Mohieddin Jafari

    Citation: BMC Bioinformatics 2019 20:73

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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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

  19. 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

    Published on:

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

  20. 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

    Published on:

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

  21. 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

    Published on:

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

  22. 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

    Published on:

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

  23. 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

    Published on:

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

  24. 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

    Published on:

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

  25. 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

    Published on:

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

  26. 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

    Published on:

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

  27. 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

    Published on:

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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

    Published on:

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

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