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MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes

Huaiqiu Zhu, Gang-Qing Hu, Yi-Fan Yang, Jin Wang, Zhen-Su She
2007 BMC Bioinformatics  
The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes.  ...  The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes.  ...  O'Brien for kindly reading and revising the manuscript. We also thank Prof. Chun-Ting Zhang for providing ZCURVE 1.0 program.  ... 
doi:10.1186/1471-2105-8-97 pmid:17367537 pmcid:PMC1847833 fatcat:pi334snxdvag5gazp5efll775e

Nestlé's research on nutrition and the human gut microbiome

Enea Rezzonico, Annick Mercenier, Ed Baetge, Scott Parkinson, Thomas Beck, Johannes le Coutre, Harald Brüssow
2015 Scientific American  
We also reviewed the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our knowledge of unclassified and poorly understood gut microbes that are undocumented  ...  in the current genome databases.  ...  A non-redundant gene set can be constructed from the predicted genes in all the assembled contigs.  ... 
doi:10.1038/scientificamerican0315-79 fatcat:rikav6kvzffi3ggxayig4d32ie

Barcodes for genomes and applications

Fengfeng Zhou, Victor Olman, Ying Xu
2008 BMC Bioinformatics  
Conclusion: These and other properties of genomes barcodes make them a new and effective tool for studying numerous genome and metagenome analysis problems.  ...  This observation has led to new and more effective ways for addressing two challenging problems: metagenome binning problem and identification of horizontally transferred genes.  ...  Department of Energy "BioEnergy Research Center" grant from the Office of Biological and Environmental Research in the DOE Office of Science, and a Distinguished Scholar grant from the Georgia Cancer Coalition  ... 
doi:10.1186/1471-2105-9-546 pmid:19091119 pmcid:PMC2621371 fatcat:vxmm6nri3re3tptb2apw6gt6aq

Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index

Kazuharu Arakawa, Haruo Suzuki, Masaru Tomita
2009 BMC Genomics  
Although this polarisation is used for computational prediction of replication origins in many bacterial genomes, the degree of GC skew visibility varies widely among different species, necessitating a  ...  Results: Here we discuss a quantitative index for the measurement of GC skew strength, named the generalised GC skew index (gGCSI), which is applicable to genomes of any length, including bacterial chromosomes  ...  Government and Tsuruoka City.  ... 
doi:10.1186/1471-2164-10-640 pmid:20042086 pmcid:PMC2804667 fatcat:ouwdocbswfdqrk2si5utzajv7q

Characterization of oligopeptide patterns in large protein sets

Anders Bresell, Bengt Persson
2007 BMC Genomics  
The methods may also be useful for detecting coding regions of genes.  ...  Recent sequencing projects and the growth of sequence data banks enable oligopeptide patterns to be characterized on a genome or kingdom level.  ...  We thank Jan-Ove Järrhed for computer support and Roland Nilsson for valuable discussions.  ... 
doi:10.1186/1471-2164-8-346 pmid:17908308 pmcid:PMC2231379 fatcat:vuxaquj7sjginbzjfoall4ikca

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

Naryttza N Diaz, Lutz Krause, Alexander Goesmann, Karsten Niehaus, Tim W Nattkemper
2009 BMC Bioinformatics  
We present a novel strategy to predict the taxonomic origin of environmental genomic fragments.  ...  For longer fragments ≥ 3 Kbp accurate predictions are made at even deeper taxonomic ranks (order and genus).  ...  The authors wish to thank Torsten Kasch, Achim Neumann, Ralf Nolte, Björn Fischer and Volker Tölle as members of the Bioinformatics Resource Facility for providing the computational and technical support  ... 
doi:10.1186/1471-2105-10-56 pmid:19210774 pmcid:PMC2653487 fatcat:e23qeugs2renhm6vkb4o6lvoie

A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement

Adriana Ravagnani, Christopher L Finan, Michael Young
2005 BMC Genomics  
The aim of this work was to search for and characterise a cognate gene family in the firmicutes (low G + C Gram-positive bacteria) and obtain information about how they may control bacterial growth and  ...  We propose that these proteins have undergone "non-orthologous domain displacement", a phenomenon akin to "non-orthologous gene displacement" that has been described previously.  ...  We are grateful to Tim Langdon and Joe Ironside for many helpful discussions and to Eugene Koonin for drawing other examples of non-orthologous domain displacement to our attention.  ... 
doi:10.1186/1471-2164-6-39 pmid:15774001 pmcid:PMC1084345 fatcat:ljdjwyrqifhm3mo3qpg6qpn3om

An unusual suspect: an uncommon human-specific synonymous coding variant within the UGT1A6 gene explains a GWAS signal and protects against bladder cancer

Wei Tang, Yi-Ping Fu, Jonine D Figueroa, Núria Malats, Montserrat Garcia-Closas, Nilanjan Chatterjee, Manolis Kogevinas, Dalsu Baris, Michael Thun, Jennifer L Hall, Immaculata De Vivo, Demetrius Albanes (+26 others)
2011 Genome Biology  
In my presentation, I will explain this work, as well as related work on autism [2] and schizophrenia [3].  ...  bacterial genomes and 87 archaeal genomes available in the RefSeq database.  ...  and archaeal genes.  ... 
doi:10.1186/1465-6906-12-s1-p19 fatcat:w7eo2r76evbkrboqtnkjm33mj4

A genetic survival network for glioblastoma multiforme

Andy Lin, Desmond J Smith
2011 Genome Biology  
This dataset provides a framework for personal genomics and is an important resource that will allow inferences of broad importance to human evolution and health.  ...  Deep exome resequencing is a powerful approach for delineating patterns of protein-coding variation among genes, pathways, individuals and populations.  ...  In my presentation, I will explain this work, as well as related work on autism [2] and schizophrenia [3]. References 1. Vissers LELM, de Ligt J, Gilissen C, Janssen I, Steehouwer M, de Vries P, van  ... 
doi:10.1186/gb-2011-12-s1-p21 fatcat:kndo5h7vg5avvbe4sk4hyck3eu

A high-throughput-sequence analysis infrastructure technology investigation framework for the evaluation of next-generation sequencing software

Xiaoyu Liu, Sumit Middha, Steven Hart, Asha Nair, Ahmed Hadad, Patrick Duffy, Jean-Pierre Kocher
2011 Genome Biology  
This dataset provides a framework for personal genomics and is an important resource that will allow inferences of broad importance to human evolution and health.  ...  Deep exome resequencing is a powerful approach for delineating patterns of protein-coding variation among genes, pathways, individuals and populations.  ...  In my presentation, I will explain this work, as well as related work on autism [2] and schizophrenia [3]. References 1. Vissers LELM, de Ligt J, Gilissen C, Janssen I, Steehouwer M, de Vries P, van  ... 
doi:10.1186/1465-6906-12-s1-p48 fatcat:ajksqqbhmrbvfpwpyb2kcwhew4

Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs

Bradford C Powell, Clyde A Hutchison
2006 BMC Bioinformatics  
"Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene prediction.  ...  We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains.  ...  We thank Morgan Giddings for computational resources and Jack Snoeyink and Craig Falls for algorithmic insights into calculating high-stringency COGs.  ... 
doi:10.1186/1471-2105-7-31 pmid:16423288 pmcid:PMC1386717 fatcat:v7eqpdcpivd6fmqt65xg2huh6u

RNA-Seq methods for imperfect samples: development, evaluation and applications

Xian Adiconis, Lin Fan, David DeLuca, Andrey Sivachenko, Nathalie Pochet, Aaron Berlin, Sarah Young, Gad Getz, Aviv Regev, Chad Nusbaum, Andreas Gnirke, Joshua Z Levin
2011 Genome Biology  
This dataset provides a framework for personal genomics and is an important resource that will allow inferences of broad importance to human evolution and health.  ...  Deep exome resequencing is a powerful approach for delineating patterns of protein-coding variation among genes, pathways, individuals and populations.  ...  In my presentation, I will explain this work, as well as related work on autism [2] and schizophrenia [3]  ... 
doi:10.1186/1465-6906-12-s1-p1 fatcat:3wqy2buosnhzhmlh32rjnaczpq

Novel purification reagents for the study of the human microbiome

George R Feehery, Eileen Dimalanta, Sriharsa Pradhan
2011 Genome Biology  
This dataset provides a framework for personal genomics and is an important resource that will allow inferences of broad importance to human evolution and health.  ...  Deep exome resequencing is a powerful approach for delineating patterns of protein-coding variation among genes, pathways, individuals and populations.  ...  In my presentation, I will explain this work, as well as related work on autism [2] and schizophrenia [3]  ... 
doi:10.1186/1465-6906-12-s1-p36 fatcat:qe4sqvcfavb2fcafrtxhkctn5i

Systems biology of bacteriophage proteins and new dimensions of the virus world discovered through metagenomics

David M Kristensen, Arcady R Mushegian, Eugene V Koonin
2011 Genome Biology  
Genome Biology 2011, 12(Suppl 1):I18 Deep exome resequencing is a powerful approach for delineating patterns of protein-coding variation among genes, pathways, individuals and populations.  ...  This dataset provides a framework for personal genomics and is an important resource that will allow inferences of broad importance to human evolution and health.  ...  In my presentation, I will explain this work, as well as related work on autism [2] and schizophrenia [3].  ... 
doi:10.1186/1465-6906-12-s1-p9 fatcat:vcospstxcrc7tc2nbsscwwbl4m

Introducing the non-B DNA Motif Search Tool (nBMST)

Regina Z Cer, Kevin H Bruce, Duncan E Donohue, Alpay N Temiz, Albino Bacolla, Uma S Mudunuri, Ming Yi, Natalia Volfovsky, Brian T Luke, Jack R Collins, Robert M Stephens
2011 Genome Biology  
Genome Biology 2011, 12(Suppl 1):I18 Deep exome resequencing is a powerful approach for delineating patterns of protein-coding variation among genes, pathways, individuals and populations.  ...  This dataset provides a framework for personal genomics and is an important resource that will allow inferences of broad importance to human evolution and health.  ...  In my presentation, I will explain this work, as well as related work on autism [2] and schizophrenia [3].  ... 
doi:10.1186/1465-6906-12-s1-p34 fatcat:e2ywi64a3vd3vdjjq6w4curlie
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