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FunCat functional inference with belief propagation and feature integration

Dimitrij Surmeli, Oliver Ratmann, Hans-Werner Mewes, Igor V. Tetko
2008 Computational biology and chemistry  
innocua. hRMN consistently outperformed two competitors for annotation of four bacterial genomes.  ...  We benchmarked this system with large-scale annotation transfer (based on the MIPS FunCat ontology) to proteins of the prokaryotes Bacillus subtilis, Helicobacter pylori, Listeria monocytogenes, and Listeria  ...  RESULTS To benchmark hRMN for automatic functional annotation, we used a dataset of four bacterial genomes, B. subtilis, H. pylori, L. monocytogenes, and L. innocua as proposed previously (Tetko, et al  ... 
doi:10.1016/j.compbiolchem.2008.06.004 pmid:18684672 fatcat:asuendsynbfyzjebn5gmchcr7i

Proteome-wide protein interaction measurements of bacterial proteins of unknown function

M. Meier, R. V. Sit, S. R. Quake
2012 Proceedings of the National Academy of Sciences of the United States of America  
Despite the enormous proliferation of bacterial genome data, surprisingly persistent collections of bacterial proteins have resisted functional annotation.  ...  In a typical genome, roughly 30% of genes have no assigned function. Many of these proteins are conserved across a large number of bacterial genomes.  ...  Despite the enormous proliferation of bacterial genome data, surprisingly persistent collections of bacterial proteins have resisted functional annotation.  ... 
doi:10.1073/pnas.1210634110 pmid:23267104 pmcid:PMC3545810 fatcat:slas7v3ltfb67nocei7ekvepqi

FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science

Heike Sichtig, Timothy Minogue, Yi Yan, Christopher Stefan, Adrienne Hall, Luke Tallon, Lisa Sadzewicz, Suvarna Nadendla, William Klimke, Eneida Hatcher, Martin Shumway, Dayanara Lebron Aldea (+6 others)
2019 Nature Communications  
We provide quality control metrics for the FDA-ARGOS genomic database resource and outline the need for genome quality gap filling in the public domain.  ...  In the first use case, we show more accurate microbial identification of Enterococcus avium from metagenomic samples with FDA-ARGOS reference genomes compared to non-curated GenBank genomes.  ...  Bacterial sequences were annotated with NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) that combines ab initio gene prediction algorithms with homology-based methods.  ... 
doi:10.1038/s41467-019-11306-6 pmid:31346170 pmcid:PMC6658474 fatcat:ek46vv5u6rghbbt6rpfhr2vuei

Functional and structural genomics using PEDANT

D. Frishman, K. Albermann, J. Hani, K. Heumann, A. Metanomski, A. Zollner, H.-W. Mewes
2001 Bioinformatics  
There is also an acute need in reliable up-to-date genomic databases integrating both functional and structural information.  ...  Results: The principal features of PEDANT are: (i) completely automatic processing of data using a wide range of bioinformatics methods, (ii) manual refinement of annotation, (iii) automatic and manual  ...  This allows to conduct automatic annotation of an average size bacterial genome in just one day.  ... 
doi:10.1093/bioinformatics/17.1.44 pmid:11222261 fatcat:ab7kex426bguhpegx6dfhn42na

Bacterial start site prediction

S. S. Hannenhalli, W. S. Hayes, A. G. Hatzigeorgiou, J. W. Fickett
1999 Nucleic Acids Research  
With the growing number of completely sequenced bacterial genes, accurate gene prediction in bacterial genomes remains an important problem.  ...  These three genomes cover a broad spectrum of bacterial genomes, since B.subtilis is a Gram-positive bacterium, E.coli is a Gram-negative bacterium and P.furiosus is an archaebacterium.  ...  Ladunga for helpful discussion on the MIP modeling. We also wish to thank the reviewers for many insightful remarks that helped improve the paper greatly.  ... 
doi:10.1093/nar/27.17.3577 pmid:10446249 pmcid:PMC148603 fatcat:ij5xsgmjiranvmbvvgcj5x5rnm

An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae

Insuk Lee, Zhihua Li, Edward M. Marcotte, Andrea Califano
2007 PLoS ONE  
Probabilistic functional gene networks are powerful theoretical frameworks for integrating heterogeneous functional genomics and proteomics data into objective models of cellular systems.  ...  Such networks provide syntheses of millions of discrete experimental observations, spanning DNA microarray experiments, physical protein interactions, genetic interactions, and comparative genomics; the  ...  a profile constructed only from bacterial genomes.  ... 
doi:10.1371/journal.pone.0000988 pmid:17912365 pmcid:PMC1991590 fatcat:qlhm3ydjzbadtoecl6wlypapay

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

Daniel Machado, Sergej Andrejev, Melanie Tramontano, Kiran Raosaheb Patil
2018 Nucleic Acids Research  
Starting with this universal model and annotated genome sequences, CarveMe uses a topdown approach to build single-species and community models in a fast and scalable manner.  ...  Finally, we create a database of 5587 bacterial models and demonstrate its potential for fast generation of microbial community models.  ...  ACKNOWLEDGEMENTS The authors would like to thank Jaime Huerta-Cepas for implementing support for BiGG annotations in eggnogmapper and Markus Herrgård for critical comments on the manuscript.  ... 
doi:10.1093/nar/gky537 pmid:30192979 pmcid:PMC6125623 fatcat:edtdezpjkndbna2oj43vzahp3e

Comparative evolutionary analysis of protein complexes in E. coli and yeast

Adam J Reid, Juan AG Ranea, Christine A Orengo
2010 BMC Genomics  
Furthermore, such complexes are involved in eukaryotic-specific functions.  ...  Results: We generated accurate, high coverage datasets of protein complexes for E. coli and yeast in order to study differences in the evolution of complexes between these two species.  ...  These complex datasets thus covered roughly 56%, and 85% of E. coli and yeast genomes respectively based on genome sizes of 3952 and 5586 genes (genome sizes were taken from Integr8 [42] ).  ... 
doi:10.1186/1471-2164-11-79 pmid:20122144 pmcid:PMC2837643 fatcat:7vn5arol5ba4nlotp7itcvumyi

WheatNet: a Genome-Scale Functional Network for Hexaploid Bread Wheat, Triticum aestivum

Tak Lee, Sohyun Hwang, Chan Yeong Kim, Hongseok Shim, Hyojin Kim, Pamela C. Ronald, Edward M. Marcotte, Insuk Lee
2017 Molecular Plant  
Sequencing Consortium MIPS annotation version 2.2.  ...  Benchmarking inferred functional linkages between wheat genes Various types of genomics data were analyzed to infer functional associations between wheat genes by using supervised machine learning, which  ... 
doi:10.1016/j.molp.2017.04.006 pmid:28450181 fatcat:sxpesz5bqngrpc2jenunx3thwu

Automated Prediction of Protein Function from Sequence [chapter]

Meghana Chitale, Troy Hawkins, Daisuke Kihara
2008 Prediction of Protein Structures, Functions, and Interactions  
Comparative genomics approaches FRpred 128 http://toolkit.tuebingen.mpg.de/frpred Prediction of protein functional residues MINER 120 http://coit-apple01.uncc.edu/MINER/ Functional residue prediction PSORT  ...  dataset.  ...  Thus, homology-based function prediction is still needed for the starting point of a genome scale annotation.  ... 
doi:10.1002/9780470741894.ch3 fatcat:oqwctmskrre5tjg4h7atjczfxu

WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum [article]

Tak Lee, Sohyun Hwang, Chan Yeong Kim, Hongseok Shim, Hyojin Kim, Pam Ronald, Edward Marcotte, Insuk Lee
2017 bioRxiv   pre-print
WheatNet was constructed by integrating 20 distinct genomics datasets, including 156,000 wheat-specific co-expression links mined from 1,929 microarray data.  ...  Here we report the generation of WheatNet, the first genome-scale functional network for T. aestivum and a companion web server (www.inetbio.org/wheatnet).  ...  Sequencing Consortium MIPS annotation version 2.2.  ... 
doi:10.1101/105098 fatcat:kkg5ly434nhsbdrdiljynqm6le

KEA3: improved kinase enrichment analysis via data integration

Maxim V Kuleshov, Zhuorui Xie, Alexandra B K London, Janice Yang, John Erol Evangelista, Alexander Lachmann, Ingrid Shu, Denis Torre, Avi Ma'ayan
2021 Nucleic Acids Research  
To benchmark the performance of KEA3, we examined whether KEA3 can predict the perturbed kinase from single-kinase perturbation followed by gene expression experiments, and phosphoproteomics data collected  ...  The KinCREEDSupdn benchmark dataset consists of gene sets extracted from 329 kinase loss-of-function/gain-of-function (LOF/GOF) human and mouse microarray experiments mined from GEO by contributors to  ...  We term this benchmarking dataset KinCREEDSupdn.  ... 
doi:10.1093/nar/gkab359 pmid:34019655 pmcid:PMC8265130 fatcat:gru3qfwaofbnvpd33jgy3nlh2e

A Domain Interaction Map Based on Phylogenetic Profiling

Philipp Pagel, Philip Wong, Dmitrij Frishman
2004 Journal of Molecular Biology  
Phylogenetic profiling is a well established method for predicting functional relations and physical interactions between proteins.  ...  The resulting domain interaction map (DIMA) can be explored directly or mapped to a genome of interest.  ...  Table 3 . 3 Accuracy of functional-link prediction evaluated against the MIPS FUNCAT annotation Sample size Sensitivity Specificity NPV PPV Dataset Pairs Proteins DIMA CLASSIC DIMA CLASSIC  ... 
doi:10.1016/j.jmb.2004.10.019 pmid:15561146 fatcat:cdaccsjknncd5jnk7yw6lx75eu

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities [article]

Daniel Machado, Sergej Andrejev, Melanie Tramontano, Kiran Raosaheb Patil
2018 bioRxiv   pre-print
Starting with this universal model and annotated genome sequences, CarveMe uses a top-down approach to build single-species and community models in a fast and scalable manner.  ...  Finally, we demonstrate the scalability of CarveMe through reconstructing 5587 bacterial models.  ...  Thus, applications of metabolic modeling lag behind the opportunities presented by the increasing number of genomics and metagenomics datasets [19] .  ... 
doi:10.1101/223198 fatcat:vnwdx3ad35a2zoy3bncx5gxwgu

Genome-enabled insights into the biology of thrips as crop pests

Dorith Rotenberg, Aaron A. Baumann, Sulley Ben-Mahmoud, Olivier Christiaens, Wannes Dermauw, Panagiotis Ioannidis, Chris G. C. Jacobs, Iris M. Vargas Jentzsch, Jonathan E. Oliver, Monica F. Poelchau, Swapna Priya Rajarapu, Derek J. Schneweis (+45 others)
2020 BMC Biology  
Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison  ...  Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.  ...  Acknowledgements We thank the staff at the Baylor College of Medicine Human Genome Sequencing Center for their contributions.  ... 
doi:10.1186/s12915-020-00862-9 pmid:33070780 fatcat:zqqwcbvquffu3jelq6rzxhtkne
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