Filters








37 Hits in 10.5 sec

Chronology-Sensitive Hierarchical Clustering of Pyrosequenced DNA Samples of E. coli: A Case Study

Aldrin Montana, Alexander Dekhtyar, Emily Neal, Michael Black, Chris Kitts
2011 2011 IEEE International Conference on Bioinformatics and Biomedicine  
This paper is a case study for the use of a modified hierarchical clustering algorithm, which takes into account the underlying structure of the bacterial DNA isolate collection to which it is applied.  ...  Hierarchical clustering is used in computational biology as a method of comparing sequenced bacterial strain DNA and determining bacterial isolates that belong to the same strain.  ...  In our case study we pyrosequenced the 23S rRNA -5S rRNA ITS region of the E. coli genome.  ... 
doi:10.1109/bibm.2011.99 dblp:conf/bibm/MontanaDNBK11 fatcat:lhd4fjuzira4xp4n2f5cy3n5la

Late-Onset Bloodstream Infection and Perturbed Maturation of the Gastrointestinal Microbiota in Premature Infants

Alexander G. Shaw, Kathleen Sim, Paul Randell, Michael J. Cox, Zoë E. McClure, Ming-Shi Li, Hugo Donaldson, Paul R. Langford, William O. C. M. Cookson, Miriam F. Moffatt, J. Simon Kroll, Jörn-Hendrik Weitkamp
2015 PLoS ONE  
Next-generation sequencing of 16S rRNA gene regions amplified by PCR from total faecal DNA was used to characterise the microbiota of faecal samples preceding diagnosis from infants with LO-BSI and controls  ...  Late-onset bloodstream infection (LO-BSI) is a common complication of prematurity, and lack of timely diagnosis and treatment can have life-threatening consequences.  ...  Tim Planche and Helen Liddy (Department of Medical Microbiology, St George's Hospital) for use of the MALDI-TOF facilities.  ... 
doi:10.1371/journal.pone.0132923 pmid:26167683 pmcid:PMC4500406 fatcat:p53nyrwmbbc5xmmv4jbkbxq7jy

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

David Laehnemann, Arndt Borkhardt, Alice Carolyn McHardy
2015 Briefings in Bioinformatics  
Both random and systematic errors can show a specific occurrence profile for each of the six prominent sequencing platforms surveyed here: 454 pyrosequencing, Complete Genomics DNA nanoball sequencing,  ...  There is a large variety of programs available for error removal in sequencing read data, which differ in the error models and statistical techniques they use, the features of the data they analyse, the  ...  Complete Genomics DNA nanoball sequencing Error information for Complete Genomics DNA nanoball sequencing comes from a systematic comparison of platforms on a human genome sample [13] .  ... 
doi:10.1093/bib/bbv029 pmid:26026159 pmcid:PMC4719071 fatcat:rxxmlzhofbhifh3vtqnro4uizu

AMMI Canada - CACMID Annual Conference

2010 Canadian Journal of Infectious Diseases and Medical Microbiology  
A Abbott B . . . . . . . . . . . . . . . . . . . . . . . . . K2 Abraham A . . . . . . . . . . . . . . . . . . . . . . P21 Adachi D . . . . . . . . . . . . . . . . . . . . . . . .  ...  P31,P32 Ammons B . . . . . . . . . . . . . . . . . . . . . . . .F7 Andonov A . . . . . . . . . . . . . . . . . . . . . . . D2 Andonova M . . . . . . . . . . . . . . . . . .  ...  The sensitivity and rapid turnaround time makes pyrosequencing a promising technology for clinical laboratories. j AHMED-BENTLEY, R vERITY DyaLIfEdx, Edmonton, AB oBjective: The purpose of this study was  ... 
doi:10.1155/2010/723876 fatcat:73ondscew5ggrly3sggs5wxfty

Abstracts

2009 Antonie van Leeuwenhoek. International Journal of General and Molecular Microbiology  
Conclusion: The limited sensitivity of the C. burnetii ELISA limits its suitability for seroprevalence studies.  ...  Unfortunately, 2007 was only a 'warming up' for 2008, in which in total more than 998 cases were found. The center of the infection moved a little to the east in North-Brabant, around Zeeland/Veghel.  ...  AC Schürch 1 , K Kremer 1 , O Daviena 1 , A Kiers 2 , MJ Boeree 3 , This project is financially supported by The Netherlands Ministry of Economic Affairs and the B-Basic partner organizations (www.b-basic.nl  ... 
doi:10.1007/s10482-009-9328-5 pmid:19343545 fatcat:vliejbeyvvhgnasah7ei7khzhe

Integrated Omics: Tools, Advances, and Future Approaches

Biswapriya B Misra, Carl D Langefeld, Michael Olivier, Laura A Cox
2018 Journal of Molecular Endocrinology  
The ultimate goal is towards the holistic realization of a 'systems biology' understanding of the biological question in hand.  ...  data files on a daily basis.  ...  To deal with sample heterogeneity, Wang and Gu (2016) have proposed three clustering categories, direct integrative clustering, clustering of clusters and regulatory integrative clustering.  ... 
doi:10.1530/jme-18-0055 pmid:30006342 fatcat:62c6xglxcbhhnkxgqo5gt7garq

International Conference on Emerging Infectious Diseases 2018 Poster and Oral Presentation Abstracts

2018 Emerging Infectious Diseases  
Stool samples were collected from six patients and tested positive for E. coli. Two samples were genotyped and were positive for STEC (shiga toxin producing E. coli).  ...  E. coli susceptibility testing showed increased prevalence of tetracycline-resistant E. coli in the agricultural watershed.  ...  There were 20 patients with diarrhea, of these, stool samples were collected from 6 and were positive for E. coli producing shiga toxin -STEC.  ... 
doi:10.3201/eid2409.nn2409 fatcat:ba2ez7c45zg2plezo64wusdcqu

Computational Genomic Signatures

Ozkan Ufuk Nalbantoglu, Khalid Sayood
2011 Synthesis Lectures on Biomedical Engineering  
Each lecture covers, for that topic, the fundamental principles in a unified manner, develops underlying concepts needed for sequential material, and progresses to more advanced topics.  ...  Lectures in Biomedical Engineering will be comprised of 75-to 150-page publications on advanced and state-of-the-art topics that spans the field of biomedical engineering, from the atom and molecule to  ...  Computational Genomic Signatures Ozkan Ufuk Nalbantoglu and Khalid Sayood 2011 Acknowledgments This work was supported, in part, by a grant from the National Institutes of Health under grant K25AI068151  ... 
doi:10.2200/s00360ed1v01y201105bme041 fatcat:uuvesakjsfdavjgoqj672wwavm

British Society for Matrix Biology Autumn 2020 Meeting: "Basement Membranes in Health and Disease"

2021 International journal of experimental pathology (Print)  
Report by The 2020 BSMB Autumn meeting was planned as an inperson get-together of matrix biologists with a focus on the important role of basement membranes in health and disease.  ...  Results: Pico-SMARTSeq2 transcriptomics on SIO cocultures revealed that IFNγ sensitizes epithelial cells to Fasmediated apoptosis.  ...  The group is also developing a second generation of CyDisCo technology, which might help in producing full length BM proteins in cytoplasm of E. coli.  ... 
doi:10.1111/iep.12381 pmid:33745160 fatcat:3avcmv2zqfcanf76tzgroud5si

Ancient DNA Analysis of the Thulamela Remains: Deciphering the Migratory Patterns of a Southern African Population

Molebogeng Bodiba, Maryna Steyn, Paulette Bloomer, Morongwa N. Mosothwane, Frank Rühli, Abigail Bouwman
2019 Journal of African Archaeology  
Poor quality and quantity of DNA meant that only haplogroups, not subhaplogroups, of the individuals could be traced.  ...  Sotho/Tswana groups) and to separate the samples into at least two genetic groups.  ...  resistance gene, which allowed the E. coli to grow.  ... 
doi:10.1163/21915784-20190017 fatcat:wzflxm346vfmdcqdzytpmpwcwm

NRSF [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
When one node is connected to several others then the clustering coefficient can be determined. The clusters may form different types of hierarchal structures.  ...  In E. coli bacteria, the volume of the nucleoid is $0.2 μ 3 within the $1 μ 3 cell. The bacterial chromosome is compacted by $10 3 -to 10 4 -fold. The DNA occupies about 5% of the nucleoid.  ...  around by about 1 and 3/4 times/particle and these nu bodies are connected with a 40-60-nucleotide long DNA linker with either histone 1 or histone 5 (▶histones).  ... 
doi:10.1007/978-1-4020-6754-9_11585 fatcat:r5ybk4fgovebphvk7xkzgr5q34

Nitrogen Cycle [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
When one node is connected to several others then the clustering coefficient can be determined. The clusters may form different types of hierarchal structures.  ...  In E. coli bacteria, the volume of the nucleoid is $0.2 μ 3 within the $1 μ 3 cell. The bacterial chromosome is compacted by $10 3 -to 10 4 -fold. The DNA occupies about 5% of the nucleoid.  ...  around by about 1 and 3/4 times/particle and these nu bodies are connected with a 40-60-nucleotide long DNA linker with either histone 1 or histone 5 (▶histones).  ... 
doi:10.1007/978-1-4020-6754-9_11438 fatcat:l3g7v7z6zbeqbcnxd5bpkr5myy

2019 | Scientific Abstracts

2019 Reproductive Sciences  
ARID1A and FOXA2 protein levels were significantly correlated in a sample set of eutopic endometrium from infertile women with endometriosis and control women based on IHC (p<0.001). 5) Similar to Pgr  ...  To establish the mechanistic role of circulating RNAs, cord plasma samples were freeze-thawed and RNase treated then supplemented to NRVMs in the presence of liposomal transfection reagent.  ...  Methods: We have designed a prospective cohort study named "Maternity Log Study" and collected blood and urine samples between 12 and 23 gestational weeks (period 1), between 24 and 34 gestational weeks  ... 
doi:10.1177/1933719119834079 pmid:31997299 fatcat:7z3ip6eu5raabfxulta2cxzo3u

Epothilones [chapter]

2015 Encyclopedia of Cancer  
This seems to be a widespread effect of 5-aza-2 0 -deoxycytidine, because all cancer cell lines studied so far are sensitive to the DNA demethylating effects of this agent.  ...  from healthy subjects using pyrosequencing.  ...  While it initially was believed that the RAF-MEK-ERK cascade depended upon stochastic interactions, studies have uncovered the existence of multiple forms of scaffolding proteins.  ... 
doi:10.1007/978-3-662-46875-3_1971 fatcat:shxqo5kunjairjqkjr5sboyw54

Early-Stage Ovarian Cancer [chapter]

Behrouz Zand, Ralph S. Freedman
2014 Encyclopedia of Cancer  
This seems to be a widespread effect of 5-aza-2 0 -deoxycytidine, because all cancer cell lines studied so far are sensitive to the DNA demethylating effects of this agent.  ...  from healthy subjects using pyrosequencing.  ...  While it initially was believed that the RAF-MEK-ERK cascade depended upon stochastic interactions, studies have uncovered the existence of multiple forms of scaffolding proteins.  ... 
doi:10.1007/978-3-662-46875-3_6895 fatcat:bvvmygwe7zcivlxjdyvoc7a7ke
« Previous Showing results 1 — 15 out of 37 results