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Lynx: a knowledge base and an analytical workbench for integrative medicine

Dinanath Sulakhe, Bingqing Xie, Andrew Taylor, Mark D'Souza, Sandhya Balasubramanian, Somaye Hashemifar, Steven White, Utpal J. Dave, Gady Agam, Jinbo Xu, Sheng Wang, T. Conrad Gilliam (+1 others)
2015 Nucleic Acids Research  
Lynx (http://lynx.ci.uchicago.edu) is a web-based database and a knowledge extraction engine.  ...  Moreover, the Lynx analytical workbench has been supplemented with new tools for reconstruction of co-expression networks and feature-and-network-based prioritization of genetic factors and molecular mechanisms  ...  ACKNOWLEDGEMENTS We would like to thank Drs Inna Dubchak and William Dobyns for their invaluable contributions to the project.  ... 
doi:10.1093/nar/gkv1257 pmid:26590263 pmcid:PMC4702889 fatcat:cfolf3lbrzhjjj4ncrjakyeozy

Efforts Towards Accessible And Reliable Bioinformatics

Matúš Kalaš, Inge Jonassen
2015 Zenodo  
The eSysbio project explored ways of developing a workbench for collaborative data analysis, accessible in various ways for users with various tasks and expertise.  ...  As diverse components are necessary for the accessible and reliable bioinformatics scenario, our work focussed in particular on the following: In the BioXSD project, we aimed at developing an XML-Schema-based  ...  Workbenches The term workbench originates from an analogy with actual workbenches for manual work.  ... 
doi:10.5281/zenodo.33715 fatcat:2pxqpqu5yvat3ctdedqam3sjsi

A scalable high-throughput targeted next-generation sequencing assay for comprehensive genomic profiling of solid tumors

Jeffrey M. Conroy, Sarabjot Pabla, Sean T. Glenn, R. J. Seager, Erik Van Roey, Shuang Gao, Blake Burgher, Jonathan Andreas, Vincent Giamo, Melissa Mallon, Yong Hee Lee, Paul DePietro (+6 others)
2021 PLoS ONE  
This has created a need for rapid, scalable comprehensive genomic profiling (CGP) systems that detect an increasing number of therapeutically-relevant variant types and molecular signatures.  ...  The supporting systems and scalable workflow allow for efficient interpretation and prompt reporting of hundreds of patient cancer genomes per week with excellent analytical performance.  ...  Acknowledgments We thank the clinical lab personnel for sample collection and processing, as well as the operations, commercial, information technology, and clinical data teams for assistance with this  ... 
doi:10.1371/journal.pone.0260089 pmid:34855780 pmcid:PMC8639101 fatcat:p5zjaxnhs5grnma4s5s4jxeuii

Multi-Platform Metabolomic Analyses of Ergosterol-Induced Dynamic Changes in Nicotiana tabacum Cells

Fidele Tugizimana, Paul A. Steenkamp, Lizelle A. Piater, Ian A. Dubery, Miyako Kusano
2014 PLoS ONE  
PCA scores plots revealed dose-and time-dependent metabolic variations, with optimal treatment conditions being found to be 300 nM ergosterol and an 18 h incubation period.  ...  Chromatographic techniques (GC-FID, GC-MS, GC6GC-TOF-MS, UHPLC-MS) and 1 H NMR spectroscopy were used for quantitative and qualitative analyses.  ...  the latter are an essential part of human life (foods, medicines, industrial raw materials, etc.) and a vital component of the whole ecosystem.  ... 
doi:10.1371/journal.pone.0087846 pmid:24498209 pmcid:PMC3909234 fatcat:ep726mqkuvbb5bokolpmenxvw4

Recent advancement in Next Generation Sequencing techniques and its computational analysis [article]

Khalid Raza, Sabahuddin Ahmad
2017 arXiv   pre-print
This novel approach is a newbie and has critical advantages over the traditional Capillary Electrophoresis (CE) based Sanger Sequencing.  ...  Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society.  ...  The first NGS technology, known as Massively Parallel Signature Sequencing (MPSS), was launched by a USA based Lynx Therapeutics Company in 2000.  ... 
arXiv:1606.05254v2 fatcat:ruu3lkfca5fetkzfg5vywzx2su

Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells [article]

John D Blischak, Ludovic Tailleux, Marsha Myrthil, Cécile Charlois, Emmanuel Bergot, Aurélien Dinh, Gloria Morizot, Olivia Chény, Cassandre Von Platen, Jean-Louis Herrmann, Roland Brosch, Luis B Barreiro (+1 others)
2017 bioRxiv   pre-print
Lastly, we trained a classifier based on the gene expression levels in the non-infected cells, and demonstrated decent performance on our data and an independent data set.  ...  Despite evidence for heritability, it is not currently possible to predict who may develop TB.  ...  Acknowledgements We thank Matthew Stephens and John Novembre for providing feedback and Gilad lab members for helpful discussion.  ... 
doi:10.1101/104729 fatcat:urdslqk63vftpkrznwvvlhc64m

Three-dimensional point-cloud room model in room acoustics simulations

Milos Markovic, So/ren K. Olesen, Dorte Hammersho/i
2013 Journal of the Acoustical Society of America  
In the present paper, we provide a new approach for treatment of boundary integrals, including hypersingular, singular, and nearly singular integrals via analytical expressions for generic boundary conditions  ...  an integral manner.  ...  This paper develops an efficient Bayesian sampling approach to geoacoustic scattering and reflection inversion based on trans-dimensional (trans-D) sampling over both the seabed model (number of sediment  ... 
doi:10.1121/1.4806371 fatcat:ln4w6j7cjvchrckf2gzfmeiwoi

Evaluation des systèmes de détection d'intrusions

-Anas -ABOU EL KALAM
2006 Revue de l Electricité et de l Electronique  
An attacker has a partial knowledge about the targeted system.  ...  Required Knowledge level Knowledge about IDS internals is not necessary; suitable for black-box evaluation A good knowledge of the structure and the design of the evaluated IDS.  ...  Analytical evaluation It is usually based on some model of the system under study not the system itself and can be done at any stage during the development cycle.  ... 
doi:10.3845/ree.2006.102 fatcat:erwecavq3zh33o3b5aemi5q5gm

MAM Volume 17 Supplement S1 - EXPO Issue

2011 Microscopy and Microanalysis  
A general knowledge of optical microscopy is helpful, but no prior knowledge of confocal microscopy is necessary to benefit from the workshop.  ...  Roberts has authored/co-authored 7 publications and participates as a liaison for university-based undergraduate courses with an industrial design project.  ... 
doi:10.1017/s1431927611012049 fatcat:ws4y2lfvxzhf5id574tcb7cw6i

Abstracts of the 7th Baltic Genetic Congress

2018 Environmental and Experimental Biology  
Acknowledgements Latvian Ministry of Agriculture and Farmers Parliament (ZSA) for financial support; Programme 'Evaluation of breeding material suitable for integrated and organic crop cultivation technologies  ...  Acknowledgements The study was conducted with the financial support of State Scientific Investigation Program "Fundamental and practical sciences for medicine" (2016-2020).  ...  species, as well as wolf, lynx and capercaillie.  ... 
doi:10.22364/eeb.16.18 fatcat:7ynirmvghzfifdhpzwnesji2oa

6th International Symposium Breeding Research on Medicinal and Aromatic Plants (BREEDMAP 6), Quedlinburg, Germany June 19 - 23, 2016 - Abstracts of Oral Presentations and Posters

Frank Marthe, Heike Riegler, Frank Marthe
2016
Lothar Ketterer and Dr. Sascha Schmidt. A part of this research has been founded by the VolkswagenStiftung and the AIF. I also want to thank Prof. H.  ...  Schulz, Quedlinburg, and his group for fruitful cooperation over many years.  ...  A detailed knowledge of flower biology is an important prerequisite for crosses and/or possible hybridization.  ... 
doi:10.5073/jka.2016.453.000 fatcat:uefjwyr6qrgvfiaabl23rdvboe

Laughter in the trenches : humour and front experience in German First World War narratives

Jakub Kazecki
2006
Furthermore, the study examines the role of humour and laughter in the construction of gender roles, with a concentration on soldier masculinity.  ...  The investigation focuses on selected diaries, novels, and short stories based on autobiographical experiences written by authors during the Great War and in the Weimar era (1919-1933): In Stahlgewittern  ...  On his way, he encounters a hungry mother lynx that is not scared of people, and has developed a taste for human flesh.  ... 
doi:10.14288/1.0100345 fatcat:ajezpmkzjzgnziz6wsoaer4lsy

Aalborg Universitet Bioinformatic Tools for Next Generation DNA Sequencing Sønderkaer, Mads Bioinformatic Tools for Next Generation DNA Sequencing Development and Analysis of Model Systems PhD thesis

Mads Sønderkaer
2012 unpublished
between three tissues, only using six samples, provided new knowledge of an already well-studied process and new target genes for further research.  ...  Top: A Read represented by a K-mer graphs (K=4), where the graph has a node for every K-mer in the read and an edge for every pair of K-mers that overlap by K-1 bases in the read.  ...  For similarity-based gene prediction, we aligned the protein sequences of four sequenced plants (A. thaliana, Carica papaya, V. vinifera and Oryza sativa) onto the potato genome using TBLASTN with an E-value  ... 
fatcat:u5dtda74fzerzljsflkxgrs5bq

The microbiota of sea turtles

TITUS FRANCISCUS SCHEELINGS
2019
The remaining chapters are focused on the microbiota of sea turtles and how it is affected by factors such as phylogeny and geography with implications for sea turtle health and physiology.  ...  This thesis contains a review chapter outlining the microbiota of vertebrates and how this is influenced by phylogenetic history.  ...  Dots represent actual values and lines represent predicted values based on the model. Values less than zero are not biologically possible for the analytes measured in this investigation.  ... 
doi:10.26180/5dc912e4e65bf fatcat:7s2ornr3r5fghk6a5dwdidxpha

18th CERN School of Computing [article]

Carlo E Vandoni
1995
This paper provides a brief summary of some of the topics being covered in the lectures on computer graphics at the CERN School of Computing.  ...  Acknowledgements Some of the material in these lectures is based on the Acknowledgements Special thanks to Mario Ruggier, co designer of WebMaker, for his suggestions and his detailed reviews of the  ...  Acknowledgements VENUS is a pilot project sponsored by the CN (Computer and Networks) and AC (Accelerators Direction) divisions, staffed by myself, plus three part-time members: Nils Høymir, Lars-Johan  ... 
doi:10.5170/cern-1995-005 fatcat:7jybanhqa5c3lnxqmyk3al72b4