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  1. Content type: Methodology article

    Reproducibility of hits from independent CRISPR or siRNA screens is poor. This is partly due to data normalization primarily addressing technical variability within independent screens, and not the technical d...

    Authors: Costa Bachas, Jasmina Hodzic, Johannes C. van der Mijn, Chantal Stoepker, Henk M. W. Verheul, Rob M. F. Wolthuis, Emanuela Felley-Bosco, Wessel N. van Wieringen, Victor W. van Beusechem, Ruud H. Brakenhoff and Renée X. de Menezes

    Citation: BMC Bioinformatics 2018 19:301

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  2. Content type: Methodology article

    Targeted resequencing with high-throughput sequencing (HTS) platforms can be used to efficiently interrogate the genomes of large numbers of individuals. A critical issue for research and applications using HT...

    Authors: Felix Francis, Michael D. Dumas, Scott B. Davis and Randall J. Wisser

    Citation: BMC Bioinformatics 2018 19:302

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  3. Content type: Software

    Here, we present an R package for entropy/variability analysis that facilitates prompt and convenient data extraction, manipulation and visualization of protein features from multiple sequence alignments. BALC...

    Authors: Alicja Płuciennik, Michał Stolarczyk, Maria Bzówka, Agata Raczyńska, Tomasz Magdziarz and Artur Góra

    Citation: BMC Bioinformatics 2018 19:300

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  4. Content type: Research

    Maize is a leading crop in the modern agricultural industry that accounts for more than 40% grain production worldwide. THe double haploid technique that uses fewer breeding generations for generating a maize ...

    Authors: Balaji Veeramani, John W. Raymond and Pritam Chanda

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2267

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  5. Content type: Research

    Novel sequence motifs detection is becoming increasingly essential in computational biology. However, the high computational cost greatly constrains the efficiency of most motif discovery algorithms.

    Authors: Shaoliang Peng, Minxia Cheng, Kaiwen Huang, YingBo Cui, Zhiqiang Zhang, Runxin Guo, Xiaoyu Zhang, Shunyun Yang, Xiangke Liao, Yutong Lu, Quan Zou and Benyun Shi

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2276

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  6. Content type: Research

    Duplication-Transfer-Loss (DTL) reconciliation is a powerful and increasingly popular technique for studying the evolution of microbial gene families. DTL reconciliation requires the use of rooted gene trees t...

    Authors: Soumya Kundu and Mukul S. Bansal

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2269

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    This article is part of a Supplement: Volume 19 Supplement 9

  7. Content type: Research

    Transcriptomic sequencing (RNA-seq) related applications allow for rapid explorations due to their high-throughput and relatively fast experimental capabilities, providing unprecedented progress in gene functi...

    Authors: Tun-Wen Pai, Kuan-Hung Li, Cing-Han Yang, Chin-Hwa Hu, Han-Jia Lin, Wen-Der Wang and Yet-Ran Chen

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2278

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  8. Content type: Research

    Top-down homogeneous multiplexed tandem mass (HomMTM) spectra are generated from modified proteoforms of the same protein with different post-translational modification patterns. They are frequently observed i...

    Authors: Kaiyuan Zhu and Xiaowen Liu

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2273

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  9. Content type: Research

    Component-based structural equation modeling methods are now widely used in science, business, education, and other fields. This method uses unobservable variables, i.e., “latent” variables, and structural equ...

    Authors: Sungtae Kim, Sungkyoung Choi, Jung-Hwan Yoon, Youngsoo Kim, Seungyeoun Lee and Taesung Park

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2270

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  10. Content type: Research

    Genome rearrangements describe changes in the genetic linkage relationship of large chromosomal regions, involving reversals, transpositions, block interchanges, deletions, insertions, fissions, fusions and tr...

    Authors: Dan Wang and Lusheng Wang

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2268

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  11. Content type: Research

    The risk factors of diabetic retinopathy (DR) were investigated extensively in the past studies, but it remains unknown which risk factors were more associated with the DR than others. If we can detect the DR ...

    Authors: Hsin-Yi Tsao, Pei-Ying Chan and Emily Chia-Yu Su

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2277

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  12. Content type: Research

    Human Microbiome Project reveals the significant mutualistic influence between human body and microbes living in it. Such an influence lead to an interesting phenomenon that many noninfectious diseases are clo...

    Authors: Jian-Yu Shi, Hua Huang, Yan-Ning Zhang, Jiang-Bo Cao and Siu-Ming Yiu

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2274

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  13. Content type: Research

    In bioinformatics, network alignment algorithms have been applied to protein-protein interaction (PPI) networks to discover evolutionary conserved substructures at the system level. However, most previous meth...

    Authors: Jianliang Gao, Bo Song, Xiaohua Hu, Fengxia Yan and Jianxin Wang

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2271

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  14. Content type: Research

    Biomedical event extraction is a crucial task in biomedical text mining. As the primary forum for international evaluation of different biomedical event extraction technologies, BioNLP Shared Task represents a...

    Authors: Lishuang Li, Jia Wan, Jieqiong Zheng and Jian Wang

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2275

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  15. Content type: Research

    Global maritime trade plays an important role in the modern transportation industry. It brings significant economic profit along with bioinvasion risk. Species translocate and establish in a non-native area th...

    Authors: Shengling Wang, Chenyu Wang, Shenling Wang and Liran Ma

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2272

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  16. Content type: Software

    The knowledge of miRNAs regulating the expression of sets of mRNAs has led to novel insights into numerous and diverse cellular mechanisms. While a single miRNA may regulate many genes, one gene can be regulat...

    Authors: Luqman Hakim Abdul Hadi, Quy Xiao Xuan Lin, Tri Tran Minh, Marie Loh, Hong Kiat Ng, Agus Salim, Richie Soong and Touati Benoukraf

    Citation: BMC Bioinformatics 2018 19:299

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  17. Content type: Software

    Taxonomic identification of plants and insects is a hard process that demands expert taxonomists and time, and it’s often difficult to distinguish on morphology only. DNA barcodes allow a rapid species discove...

    Authors: Renato Renison Moreira Oliveira, Gisele Lopes Nunes, Talvâne Glauber Lopes de Lima, Guilherme Oliveira and Ronnie Alves

    Citation: BMC Bioinformatics 2018 19:297

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  18. Content type: Software

    Microarray experiments comprise more than half of all series in the Gene Expression Omnibus (GEO). However, downloading and analyzing raw or semi-processed microarray data from GEO is not intuitive and require...

    Authors: Maria Luisa Amaral, Galina A. Erikson and Maxim N. Shokhirev

    Citation: BMC Bioinformatics 2018 19:296

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  19. Content type: Software

    Polygenic risk scores (PRS) describe the genomic contribution to complex phenotypes and consistently account for a larger proportion of variance in outcome than single nucleotide polymorphisms (SNPs) alone. Ho...

    Authors: Lawrence M. Chen, Nelson Yao, Elika Garg, Yuecai Zhu, Thao T. T. Nguyen, Irina Pokhvisneva, Shantala A. Hari Dass, Eva Unternaehrer, Hélène Gaudreau, Marie Forest, Lisa M. McEwen, Julia L. MacIsaac, Michael S. Kobor, Celia M. T. Greenwood, Patricia P. Silveira, Michael J. Meaney…

    Citation: BMC Bioinformatics 2018 19:295

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  20. Content type: Software

    Since circular RNAs (circRNAs) post-transcriptionally regulate gene expression, they have attracted increasing attention. However, there is no existing tool to annotate and extract spliced sequences for circRN...

    Authors: Shanliang Zhong, Jinyan Wang, Qian Zhang, Hanzi Xu and Jifeng Feng

    Citation: BMC Bioinformatics 2018 19:292

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  21. Content type: Software

    Changes in spatial chromatin interactions are now emerging as a unifying mechanism orchestrating the regulation of gene expression. Hi-C sequencing technology allows insight into chromatin interactions on a ge...

    Authors: John C. Stansfield, Kellen G. Cresswell, Vladimir I. Vladimirov and Mikhail G. Dozmorov

    Citation: BMC Bioinformatics 2018 19:279

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  22. Content type: Software

    Genetic epistasis is an often-overlooked area in the study of the genomics of complex traits. Genome-wide association studies are a useful tool for revealing potential causal genetic variants, but in this cont...

    Authors: Victor A. O. Carmelo, Lisette J. A. Kogelman, Majbritt Busk Madsen and Haja N. Kadarmideen

    Citation: BMC Bioinformatics 2018 19:277

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  23. Content type: Software

    While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages to use case...

    Authors: Stephen D. Shank, Steven Weaver and Sergei L. Kosakovsky Pond

    Citation: BMC Bioinformatics 2018 19:276

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  24. Content type: Research article

    Count data generated by next-generation sequencing assays do not measure absolute transcript abundances. Instead, the data are constrained to an arbitrary “library size” by the sequencing depth of the assay, a...

    Authors: Thomas P. Quinn, Tamsyn M. Crowley and Mark F. Richardson

    Citation: BMC Bioinformatics 2018 19:274

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  25. Content type: Software

    Transfer of genetic material from microbes or viruses into the host genome is known as horizontal gene transfer (HGT). The integration of viruses into the human genome is associated with multiple cancers, and ...

    Authors: Saurabh Baheti, Xiaojia Tang, Daniel R. O’Brien, Nicholas Chia, Lewis R. Roberts, Heidi Nelson, Judy C. Boughey, Liewei Wang, Matthew P. Goetz, Jean-Pierre A. Kocher and Krishna R. Kalari

    Citation: BMC Bioinformatics 2018 19:271

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  26. Content type: Methodology article

    Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. They are highly prone to repeat number variation and nucleotide mutation due to their repetitive and ...

    Authors: Devika Ganesamoorthy, Minh Duc Cao, Tania Duarte, Wenhan Chen and Lachlan Coin

    Citation: BMC Bioinformatics 2018 19:267

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  27. Content type: Software

    Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces typically reflect the ad hoc metadata specification practices of the associate...

    Authors: Syed Ahmad Chan Bukhari, Marcos Martínez-Romero, Martin J. O’ Connor, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen, Kei-Hoi Cheung and Steven H. Kleinstein

    Citation: BMC Bioinformatics 2018 19:268

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  28. Content type: Research article

    There are different and complicated associations between genes and diseases. Finding the causal associations between genes and specific diseases is still challenging. In this work we present a method to predic...

    Authors: Ryohei Eguchi, Mohammand Bozlul Karim, Pingzhao Hu, Tetsuo Sato, Naoaki Ono, Shigehiko Kanaya and Md. Altaf-Ul-Amin

    Citation: BMC Bioinformatics 2018 19:264

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  29. Content type: Methodology article

    Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombinat...

    Authors: Haojing Shao, Devika Ganesamoorthy, Tania Duarte, Minh Duc Cao, Clive J. Hoggart and Lachlan J. M. Coin

    Citation: BMC Bioinformatics 2018 19:261

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  30. Content type: Methodology article

    The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accura...

    Authors: Chi Xiao, Weifu Li, Hao Deng, Xi Chen, Yang Yang, Qiwei Xie and Hua Han

    Citation: BMC Bioinformatics 2018 19:263

    Published on:

  31. Content type: Software

    Methylated RNA immunoprecipitation sequencing (MeRIP-seq or m6A-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-Methyl-Adnosine methylation. However, due to the intrinsic pr...

    Authors: Teng Zhang, Shao-Wu Zhang, Lin Zhang and Jia Meng

    Citation: BMC Bioinformatics 2018 19:260

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  32. Content type: Methodology article

    Combining genomic data sets from multiple studies is advantageous to increase statistical power in studies where logistical considerations restrict sample size or require the sequential generation of data. How...

    Authors: Yuqing Zhang, David F. Jenkins, Solaiappan Manimaran and W. Evan Johnson

    Citation: BMC Bioinformatics 2018 19:262

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  33. Content type: Research

    The analysis of tissue-specific protein interaction networks and their functional enrichment in pathological and normal tissues provides insights on the etiology of diseases. The Pan-cancer proteomic project, ...

    Authors: Davide S. Sardina, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti and Rosalba Giugno

    Citation: BMC Bioinformatics 2018 19(Suppl 7):188

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  34. Content type: Research

    The aim of this article is to analyze the effect on biochemical recurrence and on overall survival of removing an extensive number of pelvic lymph nodes during prostate cancer surgery. The lack of evidence fro...

    Authors: Chiara Gigliarano, Alessandro Nonis, Alberto Briganti, Marco Bonetti and Clelia Di Serio

    Citation: BMC Bioinformatics 2018 19(Suppl 7):200

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  35. Content type: Research

    With ever increasing accessibility to high throughput technologies, more complex treatment structures can be assessed in a variety of ’omics applications. This adds an extra layer of complexity to the analysis...

    Authors: Kirsty L. Hassall and Andrew Mead

    Citation: BMC Bioinformatics 2018 19(Suppl 7):199

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  36. Content type: Research

    Recent advances in data analysis methods based on principles of Mendelian Randomisation, such as Egger regression and the weighted median estimator, add to the researcher’s ability to infer cause-effect links ...

    Authors: Susana Conde, Xiaoguang Xu, Hui Guo, Markus Perola, Teresa Fazia, Luisa Bernardinelli and Carlo Berzuini

    Citation: BMC Bioinformatics 2018 19(Suppl 7):195

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  37. Content type: Research

    An open challenge in translational bioinformatics is the analysis of sequenced metagenomes from various environmental samples. Of course, several studies demonstrated the 16S ribosomal RNA could be considered ...

    Authors: Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Giosue’ Lo Bosco, Giovanni Renda, Riccardo Rizzo, Salvatore Gaglio and Alfonso Urso

    Citation: BMC Bioinformatics 2018 19(Suppl 7):198

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  38. Content type: Research

    In exploring the time course of a disease to support or generate biological hypotheses, the shape of the hazard function provides relevant information. For long follow-ups the shape of hazard function may be c...

    Authors: Marco Fornili, Patrizia Boracchi, Federico Ambrogi and Elia Biganzoli

    Citation: BMC Bioinformatics 2018 19(Suppl 7):186

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

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