scholarly journals The A, C, G, and T of Genome Assembly

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Bilal Wajid ◽  
Muhammad U. Sohail ◽  
Ali R. Ekti ◽  
Erchin Serpedin
Keyword(s):  
Computational Biology ◽  
Genome Assembly ◽  
Future Research ◽  
Raw Data ◽  
Significant Research ◽  
Sequencing Platforms ◽  
Key Steps

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.

scholarly journals Open Data and the Danger of Sympathetic Magic

2017 ◽  
Author(s):  
Brian Ballsun-Stanton ◽  
Georgia Burnett
Keyword(s):  
Philosophy Of Science ◽  
Research Methodology ◽  
Open Data ◽  
Research Impact ◽  
Future Research ◽  
High Quality ◽  
Raw Data ◽  
Sympathetic Magic ◽  
Funded Research ◽  
Significant Research

This chapter provides a minimal normative framework for discussing the desired attributes of a published dataset using Lakatos’ philosophy of science and the metaphor of sympathetic magic. When researchers publish their results, journals and granting agencies increasingly want datasets opened alongside. These datasets may vary in quality, reusability, and comprehensiveness. Yet, without a clear knowledge of how the research methodology and analysis affects the production of the raw data, any future attempts to reproduce analysis will produce the same magical results only by following the same steps. While the requirement for Open Data in government funded research can provide an excellent basis for future research, not all Open Data is created equal. Releasing the methods of analysis alongside a dataset of high quality will also allow for lower technical difficulties when reusing or remixing the data. Then data, collected once, may be reused in multiple projects for a significant research impact. And to some, we can show that data is, indeed, magic.

scholarly journals A Survey on Deep Learning Based Methods and Datasets for Monocular 3D Object Detection

Electronics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 517
Author(s):  
Seong-heum Kim ◽  
Youngbae Hwang
Keyword(s):  
Deep Learning ◽  
Object Detection ◽  
Low Cost ◽  
Detection Methods ◽  
Future Research ◽  
3D Object ◽  
Practical Applications ◽  
Depth Sensors ◽  
Significant Research ◽  
3D Object Detection

Owing to recent advancements in deep learning methods and relevant databases, it is becoming increasingly easier to recognize 3D objects using only RGB images from single viewpoints. This study investigates the major breakthroughs and current progress in deep learning-based monocular 3D object detection. For relatively low-cost data acquisition systems without depth sensors or cameras at multiple viewpoints, we first consider existing databases with 2D RGB photos and their relevant attributes. Based on this simple sensor modality for practical applications, deep learning-based monocular 3D object detection methods that overcome significant research challenges are categorized and summarized. We present the key concepts and detailed descriptions of representative single-stage and multiple-stage detection solutions. In addition, we discuss the effectiveness of the detection models on their baseline benchmarks. Finally, we explore several directions for future research on monocular 3D object detection.

The Entrepreneurship Educator: Understanding Role Identity

2020 ◽  
pp. 251512742097966
Author(s):  
Birgitte Wraae ◽  
Candida Brush ◽  
Shahrokh Nikou
Keyword(s):  
Role Identity ◽  
Future Research ◽  
Analysis Tool ◽  
Perceptions Of Students ◽  
Significant Research ◽  
Future Research Directions ◽  
The Relationship ◽  
Role Identity Theory ◽  
Depth Interviews

Significant research explores effectiveness of entrepreneurial curriculum, teaching innovations and programs, but less often studied is the role of entrepreneurship educators. The way that the educator sees his or her role relative to the students is of critical importance because this directly influences pedagogy choices, expectations for students and learning outcomes, as well as job satisfaction. While recent studies propose typologies characterizing pedagogical approaches of educators, few of these are based on the data from entrepreneurship educators. Framed within role identity theory, we conducted 13 in–depth interviews to examine how entrepreneurship educators perceive their role. Using the qualitative data analysis tool (NVivo), we analyzed how the relationship between their perceptions of their role and core value orientation is connected to teaching approaches. Results show that these educators view their roles as teacher-focused, network-focused, or student-focused and that these perspectives are associated with different perceptions of students’ role and learning objectives. Further, we find different levels of emphasis on roles and that personal core values are differentially linked to these roles. Implications and future research directions are discussed.

scholarly journals Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes

Toxins ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 488 ◽  
Author(s):  
Shiyong Zhang ◽  
Jia Li ◽  
Qin Qin ◽  
Wei Liu ◽  
Chao Bian ◽  
...  
Keyword(s):  
High Throughput ◽  
Genome Assembly ◽  
Raw Materials ◽  
Pelteobagrus Fulvidraco ◽  
Yellow Catfish ◽  
High Quality ◽  
Protein Coding ◽  
Toxin Genes ◽  
Sequencing Platforms ◽  
High Quality Genome

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species.

scholarly journals Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveals expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions

2021 ◽  
pp. gr.275325.121
Author(s):  
Rodrigo P. Baptista ◽  
Yiran Li ◽  
Adam Sateriale ◽  
Karen L. Brooks ◽  
Alan Tracey ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Diarrheal Disease ◽  
Gene Copy ◽  
Future Research ◽  
Single Nucleotide Variants ◽  
Cryptosporidium Hominis ◽  
Entire Chromosome ◽  
Long Read ◽  
Subtelomeric Regions

Cryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community has only had access to a good, but incomplete, Cryptosporidium parvum IOWA reference genome sequence. Incomplete reference sequences hamper annotation, experimental design and interpretation. We have generated a new C. parvum IOWA genome assembly supported by PacBio and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species C. parvum, Cryptosporidium hominis and Cryptosporidium tyzzeri. We made 1,926 C. parvum annotation updates based on experimental evidence. They include new transporters, ncRNAs, introns and altered gene structures. The new assembly and annotation revealed a complete Dnmt2 methylase ortholog. Comparative annotation between C. parvum, C. hominis and C. tyzzeri revealed that most "missing" orthologs are found suggesting that the biological differences between the species must result from gene copy number variation, differences in gene regulation and single nucleotide variants (SNVs). Using the new assembly and annotation as reference, 190 genes are identified as evolving under positive selection, including many not detected previously. The new C. parvum IOWA reference genome assembly is larger, gap free and lacks ambiguous bases. This chromosomal assembly recovers all 16 chromosome ends, 13 of which are contiguously assembled. The three remaining chromosome ends are provisionally placed. These ends represent duplication of entire chromosome ends including subtelomeric regions revealing a new level of genome plasticity that will both inform and impact future research.

scholarly journals Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1359
Author(s):  
Esther Camacho ◽  
Sandra González-de la Fuente ◽  
Jose C. Solana ◽  
Alberto Rastrojo ◽  
Fernando Carrasco-Ramiro ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Leishmania Major ◽  
De Novo ◽  
Gene Annotation ◽  
Leishmania Species ◽  
De Novo Genome Assembly ◽  
Sequencing Platforms

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

Online Word-of-Mouth Reviews

2014 ◽  
pp. 1689-1697
Author(s):  
Jing Huo ◽  
Qinglong Gou ◽  
Qi Dai ◽  
Zhimin Huang
Keyword(s):  
Word Of Mouth ◽  
Social Network Sites ◽  
Future Research ◽  
Purchase Decision ◽  
Research Directions ◽  
Research Attention ◽  
Online Word Of Mouth ◽  
Significant Research ◽  
Future Research Directions ◽  
Antecedents And Consequences

Online word-of-mouth (WOM) has received significant research attention as the Internet has rapidly developed. Owing to specific Internet platforms such as consumer reviews sites and social network sites, online WOM spreads much more quickly and widely than traditional WOM, and that phenomenon ultimately makes online WOM play a key role in a consumer's purchase decision. In this chapter we present an overview of previous research on online WOM to facilitate future research in this area. In this review, previous researches are divided into three streams, i.e., (1) the effectiveness of online WOM, (2) the valence of online WOM, and (3) the antecedents and consequences of online WOM. Also, two possible future research directions are suggested at the end the chapter.

New Trends in Graph Mining

2010 ◽  
Vol 1 (1) ◽  
pp. 81-99 ◽  
Author(s):  
Francesco Bruno ◽  
Luigi Palopoli ◽  
Simona E. Rombo
Keyword(s):  
Computational Biology ◽  
Biological Networks ◽  
Graph Mining ◽  
Building Blocks ◽  
Biological Data ◽  
Future Research ◽  
Motif Extraction

Searching for repeated features characterizing biological data is fundamental in computational biology. When biological networks are under analysis, the presence of repeated modules across the same network (or several distinct ones) is shown to be very relevant. Indeed, several studies prove that biological networks can be often understood in terms of coalitions of basic repeated building blocks, often referred to as network motifs.This work provides a review of the main techniques proposed for motif extraction from biological networks. In particular, main intrinsic difficulties related to the problem are pointed out, along with solutions proposed in the literature to overcome them. Open challenges and directions for future research are finally discussed.

Job Seeking: The Process and Experience of Looking for a Job

2020 ◽  
Vol 7 (1) ◽  
pp. 315-337 ◽  
Author(s):  
Connie R. Wanberg ◽  
Abdifatah A. Ali ◽  
Borbala Csillag
Keyword(s):  
Social Networking ◽  
Job Search ◽  
Job Quality ◽  
Future Research ◽  
Research Attention ◽  
Job Seeking ◽  
Employment Situation ◽  
Significant Research ◽  
Job Finding ◽  
Job Search Methods

This review distills available empirical research about the process and experience of looking for a job. Job search varies according to several dimensions, including intensity, content, and temporality/persistence. Our review examines how these dimensions relate to job search success, which involves job finding as well as job quality. Because social networking and interviewing behavior have attracted significant research attention, we describe findings with respect to these two job search methods in greater detail. We provide examples of the relevance of context to job search (i.e., the job seeker's geographical region, country, and culture; the economy; the job seeker's current or past employment situation; and employer behaviors and preferences) and review research on bias in the job search. Finally, we survey work on job search interventions and conclude with an overview of pressing job search issues in need of future research.

scholarly journals Abalone Viral Ganglioneuritis

Pathogens ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 720
Author(s):  
Serge Corbeil
Keyword(s):  
Gene Expression ◽  
Diagnostic Tests ◽  
Management Strategies ◽  
Molecular Diagnostic ◽  
Economic Losses ◽  
Future Research ◽  
Abalone Species ◽  
Significant Research ◽  
Research Findings ◽  
Herpesvirus 1

Abalone viral ganglioneuritis (AVG), caused by Haliotid herpesvirus-1 (HaHV-1; previously called abalone herpesvirus), is a disease that has been responsible for extensive mortalities in wild and farmed abalone and has caused significant economic losses in Asia and Australia since outbreaks occurred in the early 2000s. Researchers from Taiwan, China, and Australia have conducted numerous studies encompassing HaHV-1 genome sequencing, development of molecular diagnostic tests, and evaluation of the susceptibility of various abalone species to AVG as well as studies of gene expression in abalone upon virus infection. This review presents a timeline of the most significant research findings on AVG and HaHV-1 as well as potential future research avenues to further understand this disease in order to develop better management strategies.

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