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https://www.readbyqxmd.com/read/28327989/using-and-understanding-cross-validation-strategies-perspectives-on-saeb-et%C3%A2-al
#1
Max A Little, Gael Varoquaux, Sohrab Saeb, Luca Lonini, Arun Jayaraman, David C Mohr, Konrad P Kording
This three-part review takes a detailed look at the complexities of cross validation, fostered by the peer review of Saeb et al.'s paper entitled The need to approximate the use-case in clinical machine learning. It contains perspectives by reviewers and by the original authors that touch upon cross-validation: the suitability of different strategies and their interpretation.
March 17, 2017: GigaScience
https://www.readbyqxmd.com/read/28327996/genome-sequencing-of-the-sweetpotato-whitefly-bemsia-tabaci-med-q
#2
Wen Xie, Chunhai Chen, Zezhong Yang, Litao Guo, Xin Yang, Dan Wang, Ming Chen, Jinqun Huang, Yanan Wen, Yang Zeng, Yating Liu, Jixing Xia, Lixia Tian, Hongying Cui, Qingjun Wu, Shaoli Wang, Baoyun Xu, Xianchun Li, Xinqiu Tan, Murad Ghanim, Baoli Qiu, Huipeng Pan, Dong Chu, Helene Delatte, M N Maruthi, Feng Ge, Xueping Zhou, Xiaowei Wang, Fanghao Wan, Yuzhou Du, Chen Luo, Fengming Yan, Evan L Preisser, Xiaoguo Jiao, Brad S Coates, Jinyang Zhao, Qiang Gao, Jinquan Xia, Ye Yin, Yong Liu, Judith K Brown, Xuguo Joe Zhou, Youjun Zhang
Background: The sweetpotato whitefly Bemisia tabaci is a highly destructive agricultural and ornamental crop pest. It damages host plants through both phloem feeding and vectoring plant pathogens. Introductions of B. tabaci are difficult to quarantine and eradicate because of its high reproductive rates, broad host plant range, and insecticide resistance. Findings: A total of 791 Gb of raw DNA sequence from whole genome shotgun sequencing, and 13 BAC pooling libraries were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries...
March 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28327987/pssmhcpan-a-novel-pssm-based-software-for-predicting-class-i-peptide-hla-binding-affinity
#3
Geng Liu, Dongli Li, Zhang Li, Si Qiu, Wenhui Li, Cheng-Chi Chao, Naibo Yang, Handong Li, Zhen Cheng, Xin Song, Le Cheng, Xiuqing Zhang, Jian Wang, Huanming Yang, Kun Ma, Yong Hou, Bo Li
Background: Predicting peptides binding affinity with human leukocyte antigen (HLA) is a crucial step in developing powerful antitumor vaccine for cancer immunotherapy. Currently available methods work quite well in predicting peptide binding affinity with HLA alleles such as HLA-A*0201, HLA-A*0101, and HLA-B*0702 in terms of sensitivity and specificity. However, quite a few types of HLA alleles that are present in majority of human populations including HLA-A*0202, HLA-A*0203, HLA-A*6802, HLA-B*5101, HLA-B*5301, HLA-B*5401 and HLA-B*5701 still cannot be predicted with satisfactory accuracy using currently available methods...
March 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28327985/the-need-to-approximate-the-use-case-in-clinical-machine-learning
#4
Sohrab Saeb, Luca Lonini, Arun Jayaraman, David C Mohr, Konrad P Kording
Background: The availability of smartphone and wearable sensor technology is leading to a rapid accumulation of human subject data, and machine learning is emerging as a technique to map that data into clinical predictions. As machine learning algorithms are increasingly used to support clinical decision making, it is vital to reliably quantify their prediction accuracy. Cross-validation is the standard approach where the accuracy of such algorithms is evaluated on data the algorithm has not seen during training...
March 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28327911/the-genome-sequence-of-the-wisent-bison-bonasus
#5
Kun Wang, Lizhong Wang, Johannes A Lenstra, Jianbo Jian, Yongzhi Yang, Quanjun Hu, Deyong Lai, Qiang Qiu, Tao Ma, Zheng Du, Richard Abbott, Jianquan Liu
Background: The wisent, also known as the European bison, was rescued from extinction approximately 80 years ago through the conservation of 12 individuals. Here, we present the draft genome sequence of a male wisent individual descended from this founding stock. Findings: A total of 366 billion base pairs (Gb) of raw reads from whole-genome sequencing of this wisent were generated using the Illumina HiSeq2000 platform. The final genome assembly (2.58 Gb) is composed of 29,074 scaffolds with an N50 of 4...
March 10, 2017: GigaScience
https://www.readbyqxmd.com/read/28327945/enhancing-knowledge-discovery-from-cancer-genomics-data-with-galaxy
#6
Marco A Albuquerque, Bruno M Grande, Elie J Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K Grewal, Sohrab P Shah, Paul C Boutros, Ryan D Morin
The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data...
March 9, 2017: GigaScience
https://www.readbyqxmd.com/read/28327967/genome-sequence-of-pacific-abalone-haliotis-discus-hannai-the-first-draft-genome-in-family-haliotidae
#7
Bo-Hye Nam, Woori Kwak, Young-Ok Kim, Dong-Gyun Kim, Hee Jeong Kong, Woo-Jin Kim, Jeong-Ha Kang, Jung Youn Park, Cheul Min An, Ji-Young Moon, Choul Ji Park, Jae Woong Yu, Joon Yoon, Minseok Seo, Kwondo Kim, Duk Kyung Kim, SaetByeol Lee, Samsun Sung, Chul Lee, Younhee Shin, Myunghee Jung, Byeong-Chul Kang, Shin Ga-Hee, Sojeong Ka, Kelsey Caetano-Anolles, Seoae Cho, Heebal Kim
Background: Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [1]. Abalone is an economically important fishery and aquaculture animal which is considered a highly-prized seafood delicacy...
March 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28327935/science-in-the-cloud-sic-a-use-case-in-mri-connectomics
#8
Gregory Kiar, Krzysztof J Gorgolewski, Dean Kleissas, William Gray Roncal, Brian Litt, Brian Wandell, Russel A Poldrack, Martin Wiener, R Jacob Vogelstein, Randal Burns, Joshua T Vogelstein
Modern technologies are enabling scientists to collect extraordinary amounts of complex and sophisticated data across a huge range of scales like never before. With this onslaught of data, we can allow the focal point to shift from data collection to data analysis. Unfortunately, lack of standardized sharing mechanisms and practices often make reproducing or extending scientific results very difficult. With the creation of data organization structures and tools which drastically improve code portability, we now have the opportunity to design such a framework for communicating extensible scientific discoveries...
March 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28328004/red-ml-a-novel-effective-rna-editing-detection-method-based-on-machine-learning
#9
Heng Xiong, Dongbing Liu, Qiye Li, Mengyue Lei, Liqin Xu, Liang Wu, Zongji Wang, Shancheng Ren, Wangsheng Li, Min Xia, Lihua Lu, Haorong Lu, Yong Hou, Shida Zhu, Xin Liu, Yinghao Sun, Jian Wang, Huanming Yang, Kui Wu, Xun Xu, Leo J Lee
Background: With the advancement of second generation sequencing techniques, our ability to detect and quantify RNA editing on a global scale has been vastly improved. As a result, RNA editing is now being studied under a growing number of biological conditions so that its biochemical mechanisms and functional roles can be further understood. However, a major barrier that prevents RNA editing from being a routine RNA-seq analysis, similar to gene expression and splicing analysis for example, is the lack of user-friendly and effective computational tools...
March 2, 2017: GigaScience
https://www.readbyqxmd.com/read/28327946/draft-genome-of-the-northern-snakehead-channa-argus
#10
Jian Xu, Chao Bian, Kunci Chen, Guiming Liu, Yanliang Jiang, Qing Luo, Xinxin You, Wenzhu Peng, Jia Li, Yu Huang, Yunhai Yi, Chuanju Dong, Hua Deng, Songhao Zhang, Hanyuan Zhang, Qiong Shi, Peng Xu
Background: The Northern snakehead ( Channa argus ), a member of the Channidae family of the Perciformes, and is an economically important freshwater fish native to East Asia. In North America, it has become notorious as an intentionally released invasive species. Its ability to breathe air with gills and migrate short distances over land makes it a good model for bimodal breath research. Therefore, recent research has focused on the identification of relevant candidate genes. Here, we performed whole genome sequencing of C...
March 2, 2017: GigaScience
https://www.readbyqxmd.com/read/28327993/stepwise-distributed-open-innovation-contests-for-software-development-acceleration-of-genome-wide-association-analysis
#11
Andrew Hill, Po-Ru Loh, Ragu B Bharadwaj, Pascal Pons, Jingbo Shang, Eva Guinan, Karim Lakhani, Iain Kilty, Scott A Jelinsky
BACKGROUND: The association of differing genotypes with disease related phenotypic traits offers great potential to both help identify new therapeutic targets and support stratification of patients who would gain the greatest benefit from specific drug classes. Development of low cost genotyping and sequencing has made collecting large scale genotyping data routine in population and therapeutic intervention studies. In addition, a range of new technologies are being used to capture numerous new and complex phenotypic descriptors...
February 28, 2017: GigaScience
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#12
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327966/de-novo-transcriptome-assemblies-of-four-xylem-sap-feeding-insects
#13
Erica E Tassone, Charles C Cowden, S J Castle
Background: Spittle bugs and sharpshooters are well-known xylem sap-feeding insects and vectors of the phytopathogenic bacterium Xylella fastidiosa (Wells), a causal agent of Pierce's disease of grapevines and other crop diseases. Specialized feeding on nutrient-deficient xylem sap is relatively rare among insect herbivores, and only limited genomic and transcriptomic information has been generated for xylem-sap feeders. To develop a more comprehensive understanding of biochemical adaptations and symbiotic relationships that support survival on a nutritionally austere dietary source, transcriptome assemblies for three sharpshooter species and one spittlebug species were produced...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327957/nanosim-nanopore-sequence-read-simulator-based-on-statistical-characterization
#14
Chen Yang, Justin Chu, René L Warren, Inanç Birol
Background: The MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing - valuable features for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, output of which could be used to benchmark analysis tools. Findings: Here, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327954/genome-sequencing-of-the-winged-midge-parochlus-steinenii-from-the-antarctic-peninsula
#15
Sanghee Kim, Mijin Oh, Woongsic Jung, Joonho Park, Han-Gu Choi, Seung Chul Shin
Background: In the Antarctic, only two species of Chironomidae occur naturally-the wingless midge, Belgica antarctica , and the winged midge, Parochlus steinenii . B. antarctica is an extremophile with unusual adaptations. The larvae of B. antarctica are desiccation- and freeze-tolerant and the adults are wingless. Recently, the compact genome of B. antarctica was reported and it is the first Antarctic eukaryote to be sequenced. Although P. steinenii occurs naturally in the Antarctic with B...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327943/whole-genome-sequencing-of-chinese-clearhead-icefish-protosalanx-hyalocranius
#16
Kai Liu, Dongpo Xu, Jia Li, Chao Bian, Jinrong Duan, Yanfeng Zhou, Minying Zhang, Xinxin You, Yang You, Jieming Chen, Hui Yu, Gangchun Xu, Di-An Fang, Jun Qiang, Shulun Jiang, Jie He, Junmin Xu, Qiong Shi, Zhiyong Zhang, Pao Xu
Background: Chinese clearhead icefish, Protosalanx hyalocranius , is a representative icefish species with economic importance and special appearance. Due to its great economic values in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327936/guidock-vnc-using-a-graphical-desktop-sharing-system-to-provide-a-browser-based-interface-for-containerized-software
#17
Varun Mittal, Ling-Hong Hung, Jayant Keswani, Daniel Kristiyanto, Sung Bong Lee, Ka Yee Yeung
Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line based tool and many bioinformatics pipelines consist of components that require a graphical user interface. Findings: We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327918/developmental-coordination-disorder-in-children-experimental-work-and-data-annotation
#18
Lukas Vareka, Petr Bruha, Roman Moucek, Pavel Mautner, Ladislav Cepicka, Irena Holeckova
Background: Developmental coordination disorder (DCD) is described as a motor skill disorder characterized by a marked impairment in the development of motor coordination abilities that significantly interferes with performance of daily activities and/or academic achievement. Since some electrophysiological studies suggest differences between children with/without motor development problems, we prepared an experimental protocol and performed electrophysiological experiments with the aim to make a step towards a possible diagnosis of this disorder using the event-related potentials (ERP) technique...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327913/the-use-of-oxford-nanopore-native-barcoding-for-complete-genome-assembly
#19
Sion C Bayliss, Vicky L Hunt, Maho Yokoyama, Harry A Thorpe, Edward J Feil
Background: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short-read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short-read data...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327910/phenobook-an-open-source-software-for-phenotypic-data-collection
#20
Juan M Crescente, Fabio Guidobaldi, Melina Demichelis, Maria B Formica, Marcelo Helguera, Leonardo S Vanzetti
Background: Research projects often involves observation, registration and data processing starting from information obtained in field experiments. In many cases these tasks are carried out by several persons in different places, times and ways adding different levels of complexity and error in data collecting. Furthermore, data processing can be time consuming and input errors may produce unwanted results. Main text: We have developed a novel, open source software called Phenobook, an easy, flexible and intuitive tool to organize, collect and save experimental data for further analyses...
February 24, 2017: GigaScience
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