HirBin: high-resolution identification of differentially abundant functions in metagenomes
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Erik Kristiansson | Tobias Österlund | Viktor Jonsson | E. Kristiansson | Tobias Österlund | Viktor Jonsson
[1] David R. Riley,et al. CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing , 2011, BMC Bioinformatics.
[2] Susannah G. Tringe,et al. FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus , 2014, Nucleic acids research.
[3] Georgios A. Pavlopoulos,et al. Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies , 2015, Bioinformatics and biology insights.
[4] E. Kristiansson,et al. Tentacle: distributed quantification of genes in metagenomes , 2015, GigaScience.
[5] Scott Ferson,et al. Accounting for uncertainty in DNA sequencing data. , 2015, Trends in genetics : TIG.
[6] Neil Moore,et al. A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction , 2016, BMC Genomics.
[7] Erik Kristiansson,et al. Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics , 2016, BMC Genomics.
[8] Intawat Nookaew,et al. Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue , 2014, PLoS Comput. Biol..
[9] P. Christen,et al. Aminotransferases: demonstration of homology and division into evolutionary subgroups. , 1993, European journal of biochemistry.
[10] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[11] Rick L. Stevens,et al. Unlocking the potential of metagenomics through replicated experimental design , 2012, Nature Biotechnology.
[12] O. White,et al. Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.
[13] Owen White,et al. The TIGRFAMs database of protein families , 2003, Nucleic Acids Res..
[14] S. Schuster,et al. Integrative analysis of environmental sequences using MEGAN4. , 2011, Genome research.
[15] J. Clemente,et al. Human gut microbiome viewed across age and geography , 2012, Nature.
[16] Bijay Singh,et al. An ll-Diaminopimelate Aminotransferase Defines a Novel Variant of the Lysine Biosynthesis Pathway in Plants1[W] , 2005, Plant Physiology.
[17] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.
[18] Cathy H. Wu,et al. UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..
[19] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[20] Erik Kristiansson,et al. ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes , 2009, Bioinform..
[21] E. Plummer,et al. A Comparison of Three Bioinformatics Pipelines for the Analysis ofPreterm Gut Microbiota using 16S rRNA Gene Sequencing Data , 2015 .
[22] P. Bork,et al. A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.
[23] Sean R. Eddy,et al. Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..
[24] Tao Cai,et al. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary , 2005, Bioinform..
[25] Qiang Feng,et al. A metagenome-wide association study of gut microbiota in type 2 diabetes , 2012, Nature.
[26] I. Nookaew,et al. Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods , 2013, Nucleic acids research.
[27] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[28] P. Bork,et al. Enterotypes of the human gut microbiome , 2011, Nature.
[29] InSong Koh,et al. Deciphering the human microbiome using next-generation sequencing data and bioinformatics approaches. , 2015, Methods.
[30] S. Tringe,et al. Comparative Metagenomics of Microbial Communities , 2004, Science.
[31] Robert C. Edgar,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .
[32] M. Metzker. Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.
[33] Tulika Prakash,et al. Functional assignment of metagenomic data: challenges and applications , 2012, Briefings Bioinform..
[34] Christian von Mering,et al. Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale , 2014, PLoS Comput. Biol..
[35] Aaron R. Quinlan,et al. BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..
[36] Peer Bork,et al. MOCAT2: a metagenomic assembly, annotation and profiling framework , 2016, Bioinform..
[37] S. O’Brien,et al. SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations , 2015, GigaScience.
[38] Tungadri Bose,et al. COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets , 2015, PloS one.
[39] T. Thomas,et al. Bacterial community assembly based on functional genes rather than species , 2011, Proceedings of the National Academy of Sciences.
[40] E. Kristiansson,et al. Integrative analysis of omics data. , 2017, Methods.
[41] S. Tringe,et al. Tackling soil diversity with the assembly of large, complex metagenomes , 2014, Proceedings of the National Academy of Sciences.
[42] Darren A. Natale,et al. The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.
[43] Jens Roat Kultima,et al. An integrated catalog of reference genes in the human gut microbiome , 2014, Nature Biotechnology.
[44] D. Raoult,et al. The human gut microbiome, a taxonomic conundrum. , 2015, Systematic and applied microbiology.
[45] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[46] David A. Lee,et al. Predicting protein function from sequence and structure , 2007, Nature Reviews Molecular Cell Biology.
[47] F. Corpet. Multiple sequence alignment with hierarchical clustering. , 1988, Nucleic acids research.
[48] D. Antonopoulos,et al. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. , 2010, Cold Spring Harbor protocols.