scholarly journals Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates

2016 ◽  
Vol 11 (3) ◽  
pp. 626-640 ◽  
Author(s):  
Po-Hsiang Wang ◽  
Shuiquan Tang ◽  
Kayla Nemr ◽  
Robert Flick ◽  
Jun Yan ◽  
...  
Keyword(s):  
Experimental Annotation

scholarly journals ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

2010 ◽  
Vol 26 (18) ◽  
pp. 2354-2356 ◽  
Author(s):  
P. Rocca-Serra ◽  
M. Brandizi ◽  
E. Maguire ◽  
N. Sklyar ◽  
C. Taylor ◽  
...  
Keyword(s):  
Community Level ◽  
Software Suite ◽  
Experimental Annotation

scholarly journals Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays

2010 ◽  
Vol 11 (7) ◽  
pp. R71 ◽  
Author(s):  
Adnane Sellam ◽  
Hervé Hogues ◽  
Christopher Askew ◽  
Faiza Tebbji ◽  
Marco van het Hoog ◽  
...  
Keyword(s):  
Candida Albicans ◽  
High Resolution ◽  
Human Pathogen ◽  
Tiling Arrays ◽  
Experimental Annotation ◽  
Human Pathogen Candida Albicans

scholarly journals SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions

2019 ◽  
Vol 35 (22) ◽  
pp. 4794-4796 ◽  
Author(s):  
Qingzhen Hou ◽  
Paul F G De Geest ◽  
Christian J Griffioen ◽  
Sanne Abeln ◽  
Jaap Heringa ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Sequence Data ◽  
Supplementary Information ◽  
Protein Protein Interactions ◽  
Interaction Sites ◽  
Expert User ◽  
Interaction Interface ◽  
Experimental Annotation ◽  
Protein Sequence Data

Abstract Motivation Interpretation of ubiquitous protein sequence data has become a bottleneck in biomolecular research, due to a lack of structural and other experimental annotation data for these proteins. Prediction of protein interaction sites from sequence may be a viable substitute. We therefore recently developed a sequence-based random forest method for protein–protein interface prediction, which yielded a significantly increased performance than other methods on both homomeric and heteromeric protein–protein interactions. Here, we present a webserver that implements this method efficiently. Results With the aim of accelerating our previous approach, we obtained sequence conservation profiles by re-mastering the alignment of homologous sequences found by PSI-BLAST. This yielded a more than 10-fold speedup and at least the same accuracy, as reported previously for our method; these results allowed us to offer the method as a webserver. The web-server interface is targeted to the non-expert user. The input is simply a sequence of the protein of interest, and the output a table with scores indicating the likelihood of having an interaction interface at a certain position. As the method is sequence-based and not sensitive to the type of protein interaction, we expect this webserver to be of interest to many biological researchers in academia and in industry. Availability and implementation Webserver, source code and datasets are available at www.ibi.vu.nl/programs/serendipwww/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Experimental annotation of the human genome using microarray technology

Nature ◽  
2001 ◽  
Vol 409 (6822) ◽  
pp. 922-927 ◽  
Author(s):  
D. D. Shoemaker ◽  
E. E. Schadt ◽  
C. D. Armour ◽  
Y. D. He ◽  
P. Garrett-Engele ◽  
...  
Keyword(s):  
Human Genome ◽  
Microarray Technology ◽  
Experimental Annotation

scholarly journals Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Charles Ansong ◽  
Nikola Tolić ◽  
Samuel O Purvine ◽  
Steffen Porwollik ◽  
Marcus Jones ◽  
...  
Keyword(s):  
Salmonella Typhimurium ◽  
Coding Regions ◽  
Experimental Annotation

scholarly journals Global identification of functional microRNA::mRNA interactions in Drosophila

2018 ◽  
Author(s):  
Hans-Hermann Wessels ◽  
Svetlana Lebedeva ◽  
Antje Hirsekorn ◽  
Neelanjan Mukherjee ◽  
Uwe Ohler
Keyword(s):  
Mirna Target ◽  
Signal To Noise Ratio ◽  
Absolute Quantification ◽  
Mediated Effects ◽  
Target Sites ◽  
Experimental Annotation ◽  
Global Identification ◽  
And Function

AbstractMicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. Although Drosophila has been of critical importance for miRNA discovery, biogenesis and function, there has been no comprehensive experimental annotation of functional miRNA target sites. To close this gap, we generated the first in vivo map of miRNA::mRNA interactions in Drosophila melanogaster, making use of crosslinked nucleotides in Argonaute (AGO) crosslinking and immunoprecipitation (CLIP) experiments that enable an unambiguous assignment of miRNAs to AGO binding sites at much higher signal-to-noise ratio than computational predictions alone.Absolute quantification of cellular miRNA levels showed the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two different CLIP approaches, we identified a similar predictive potential to unambiguously assign thousands of miRNA::mRNA pairs from AGO1 interaction data at unprecedented depth. Quantitative RNA-Seq and subcodon-resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites as well as their quantitative functional impact in Drosophila.

Experimental annotation of channel catfish virus by probabilistic proteogenomic mapping

PROTEOMICS ◽  
2009 ◽  
Vol 9 (10) ◽  
pp. 2634-2647 ◽  
Author(s):  
Dusan Kunec ◽  
Bindu Nanduri ◽  
Shane C. Burgess
Keyword(s):  
Channel Catfish ◽  
Channel Catfish Virus ◽  
Experimental Annotation ◽  
Proteogenomic Mapping
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