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Abbreviation : WGS
Long Form : whole-genome shotgun
No. Year Title Co-occurring Abbreviation
2019 Characterization of a Novel Ourmia-Like Mycovirus Infecting Magnaporthe oryzae and Implications for Viral Diversity and Evolution. ESTdb, GSS, MOLV4, ORF, RdRp, TSA
2019 GenBank. DDBJ, ENA, EST, GSS
2019 Iterative Variable Gene Discovery from Whole Genome Sequencing with a Bootstrapped Multiresolution Algorithm. ---
2019 Machine Learning as an Effective Method for Identifying True Single Nucleotide Polymorphisms in Polyploid Plants. SNP-ML, SNP-MLer, SNPs
2018 Chemical and genomic diversity of six Lonicera species occurring in Korea. ---
2018 Data on genome sequencing, analysis and annotation of a pathogenic Bacillus cereus 062011msu. ---
2018 Deep learning models for bacteria taxonomic classification of metagenomic data. AMP, CNN, DBN, SG
2018 Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations. PCBs, TCA
2018 Microbiome dynamics and adaptation of expression signatures during methane production failure and process recovery. ---
10  2018 Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea. TD
11  2017 16SPIP: a comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing. ---
12  2017 De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences. ---
13  2017 GenBank. DDBJ, ENA
14  2017 Genome resources for climate-resilient cowpea, an essential crop for food security. BAC
15  2017 High-throughput automated microfluidic sample preparation for accurate microbial genomics. ---
16  2017 KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies. KAT, NGS, QC
17  2017 Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus. mtDNA
18  2017 Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement. rDNA
19  2016 A functional genomics tool for the Pacific bluefin tuna: Development of a 44K oligonucleotide microarray from whole-genome sequencing data for global transcriptome analysis. ESTs, LPS, oligo-array, PBLs, PBT
20  2016 Bioinformatics Tools for Proteomics Data Interpretation. NGS, PTMs, UniProtKB
21  2016 Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. MH63, ZS97
22  2016 Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. ---
23  2016 Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions. MYA
24  2016 Draft Genome Sequence of Lactobacillus plantarum CRL1506, an Immunomodulatory Strain Isolated from Goat Milk. ---
25  2016 GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis. FMT, GUTSS
26  2016 Improvement of barley genome annotations by deciphering the Haruna Nijo genome. FL
27  2016 Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota. CAFTs, NMF
28  2016 Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture (Xaj-pitha) of Assam, India. LAB
29  2016 Signatures of Crested Ibis MHC Revealed by Recombination Screening and Short-Reads Assembly Strategy. MHC, OR
30  2016 The Metagenome of Utricularia gibba's Traps: Into the Microbial Input to a Carnivorous Plant. Ugt
31  2015 ConPADE: genome assembly ploidy estimation from next-generation sequencing data. ---
32  2015 Functional characterisation of a TLR accessory protein, UNC93B1, in Atlantic salmon (Salmo salar). PAMPs, SHK-1, TLRs
33  2015 Identification and functional analysis of genome mutations in a fluoride-resistant Streptococcus mutans strain. SNPs
34  2015 Robustness of Massively Parallel Sequencing Platforms. HTS
35  2015 Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads. NGS, TEs
36  2014 Genetic anchoring of whole-genome shotgun assemblies. ---
37  2014 Identification and characterisation of TLR18-21 genes in Atlantic salmon (Salmo salar). ISAV, PKD, TLR
38  2014 Prophage-like elements present in Mycobacterium genomes. ---
39  2014 RepARK--de novo creation of repeat libraries from whole-genome NGS reads. NGS
40  2014 Single haplotype assembly of the human genome from a hydatidiform mole. ---
41  2014 Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. BACs, CDS, ESTs, MF, SNPs, UF
42  2014 The placenta harbors a unique microbiome. ---
43  2013 A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. HMP
44  2013 GenBank. DDBJ, ENA
45  2013 Identification and characterization of TLR7, TLR8a2, TLR8b1 and TLR8b2 genes in Atlantic salmon (Salmo salar). LRRs, SHK-1, ssRNA, TLR
46  2013 Phenotypic heterogeneity of genomically-diverse isolates of Streptococcus mutans. CSP
47  2012 Alterations in the porcine colon microbiota induced by the gastrointestinal nematode Trichuris suis. VOCs
48  2012 Analysis of the salivary microbiome using culture-independent techniques. ---
49  2012 GenBank. DDBJ, ENA
50  2012 High throughput mining and characterization of microsatellites from common carp genome. BES
51  2012 High throughput sequencing methods for microbiome profiling: application to food animal systems. ---
52  2011 Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes. ---
53  2011 Functional metagenomics of methylotrophs. ---
54  2011 GenBank. DDBJ, ENA
55  2011 High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum. COs, GS FLX, NCO
56  2011 Metagenome plasticity of the bovine abomasal microbiota in immune animals in response to Ostertagia ostertagi infection. OTU
57  2011 Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. ---
58  2011 Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. ---
59  2011 Tandemly repeated DNA families in the mouse genome. TR
60  2010 GenBank. ---
61  2010 Novel non-autonomous transposable elements on W chromosome of the silkworm, Bombyx mori. LTR
62  2010 Novel non-autonomous transposable elements on W chromosome of the silkworm, Bombyx mori. LTR
63  2010 The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. ---
64  2010 [Mouse centromeric tandem repeats in silico and in situ]. CEN, MaSat, MiSat, periCEN, TRF
65  2009 A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence. GEM, SFP
66  2009 Artifacts of the 1.9x feline genome assembly derived from the feline-specific satellite sequence. LINEs, SINEs
67  2009 Bos taurus genome assembly. ---
68  2009 Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre. ---
69  2009 Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia). EST, SSRs
70  2009 The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. ESTs, SAMS
71  2009 tRNADB-CE: tRNA gene database curated manually by experts. ---
72  2008 Consensus generation and variant detection by Celera Assembler. ---
73  2008 High-resolution metagenomics targets specific functional types in complex microbial communities. SIP
74  2008 Improving Phrap-based assembly of the rat using "reliable" overlaps. ---
75  2008 Marked variation in predicted and observed variability of tandem repeat loci across the human genome. TR
76  2008 PABS: an online platform to assist BAC-by-BAC sequencing projects. PABS
77  2008 Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing. GSOM, SOM
78  2007 Genome Annotation Resource Fields--GARFIELD: a genome browser for Felis catus. ABCC, GARFIELD, NCI
79  2007 Microsatellite flanking region similarities among different loci within insect species. ---
80  2007 PigGIS: Pig Genomic Informatics System. ESTs, PigGIS, SNPs
81  2007 Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. CA, kb, MRSA, MSSA
82  2006 A second-generation integrated map of the silkworm reveals synteny and conserved gene order between lepidopteran insects. BAC, ESTs, LGs, STSs
83  2006 Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. ---
84  2006 Primate genomes. ---
85  2006 U6 snRNA variants isolated from the posterior silk gland of the silk moth Bombyx mori. PSG, snRNA
86  2005 The silk moth Bombyx mori U1 and U2 snRNA variants are differentially expressed. SG
87  2004 A preprocessor for shotgun assembly of large genomes. ---
88  2004 Comparative analysis of the Borrelia garinii genome. ---
89  2004 Fosmid-based physical mapping of the Histoplasma capsulatum genome. ---
90  2004 Shotgun sequence assembly and recent segmental duplications within the human genome. ---
91  2004 Single nucleotide polymorphisms associated with rat expressed sequences. EST, SNPs
92  2004 The Atlas genome assembly system. ---
93  2004 The genome sequence of silkworm, Bombyx mori. ESTs
94  2003 A comparative analysis of HGSC and Celera human genome assemblies and gene sets. HGSC, HS
95  2003 Chicken genome sequence: a centennial gift to poultry genetics. BAC
96  2003 Mouse SCO-spondin, a gene of the thrombospondin type 1 repeat (TSR) superfamily expressed in the brain. CSF, dpc, ISH, LDLR, RF, SCO
97  2003 The Drosophila melanogaster genome. cDNA, EST
98  2003 The phusion assembler. ---
99  2002 Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. BACs, bp
100  2002 On the sequencing of the human genome. HGP