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1. Full Text Insights from 20 years of bacterial genome sequencing
by Land, Miriam and Hauser, Loren and Jun, Se-Ran and Nookaew, Intawat and Leuze, Michael R and Ahn, Tae-Hyuk and Karpinets, Tatiana and Lund, Ole and Kora, Guruprased and Wassenaar, Trudy and Poudel, Suresh and Ussery, David W and Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Functional and Integrative Genomics, ISSN 1438-793X, 2015, Volume 15, Issue 2, pp. 141 - 161
Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA... 
Metagenomics | Next-generation sequencing | Core-genome | Pan-genome | Comparative genomics | Bacteria | Bacterial genomes | CRISPR-CAS SYSTEMS | PATHWAY/GENOME DATABASES | ESCHERICHIA-COLI | METABOLIC PATHWAYS | HUMAN GUT MICROBIOME | DEFENSE SYSTEMS | ARCHAEA | METACYC DATABASE | GENETICS & HEREDITY | 16S RIBOSOMAL-RNA | BIOCYC COLLECTION | Genetic Variation | Genome, Bacterial | Codon | Genome Size | Genomics | Molecular Sequence Annotation | Bacterial Proteins - genetics | Bacteria - classification | Phylogeny | Sequence Analysis, DNA | Analysis | Escherichia coli | Genomes | Nucleotide sequencing | Bacterial genetics | Methylation | DNA sequencing | Genetic diversity | BASIC BIOLOGICAL SCIENCES | Next-Generation Sequencing | Review
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2. Full Text BPGA-an ultra-fast pan-genome analysis pipeline
by Chaudhari, Narendrakumar M and Gupta, Vinod Kumar and Dutta, Chitra
Scientific Reports, ISSN 2045-2322, 04/2016, Volume 6, Issue 1, p. 24373
Recent advances in ultra-high-throughput sequencing technology and metagenomics have led to a paradigm shift in microbial genomics from few genome comparisons... 
STRAINS | CORE | STREPTOCOCCUS-PNEUMONIAE | EVOLUTION | MULTIDISCIPLINARY SCIENCES | SEQUENCE | VACCINE | PANGENOME | IDENTIFICATION | REVEALS | INSIGHTS | Streptococcus pyogenes - genetics | Genome, Bacterial | Software | Phylogeny | Streptococcus pyogenes - classification | High-Throughput Nucleotide Sequencing - methods | Next-generation sequencing | Genes | Computer applications | Gene pool | Genomes | Multilocus sequence typing | Gene mapping | Strains (organisms)
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3. Full Text Rare Variants Create Synthetic Genome-Wide Associations
by Dickson, Samuel P and Wang, Kai and Krantz, Ian and Hakonarson, Hakon and Goldstein, David B
PLoS Biology, ISSN 1544-9173, 01/2010, Volume 8, Issue 1, p. e1000294
Genome-wide association studies (GWAS) have now identified at least 2,000 common variants that appear associated with common diseases or related traits... 
POPULATION | NONSYNDROMIC HEARING IMPAIRMENT | GENE | BIOCHEMISTRY & MOLECULAR BIOLOGY | HIP OSTEOARTHRITIS | SUSCEPTIBILITY | BIOLOGY | DEAFNESS | SICKLE-CELL-DISEASE | AFRICAN-AMERICANS | CORE PROMOTER POLYMORPHISM | REGION | Hearing Loss - genetics | Genetic Predisposition to Disease | Genome-Wide Association Study | Humans | Risk Factors | Probability | Genotype | Polymorphism, Single Nucleotide | Anemia, Sickle Cell - genetics | Studies | Genealogy | Disease | Genetics | Genomes | Mutation | Hearing impairment | Logistics
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4. Full Text Ten years of pan-genome analyses
by Vernikos, George and Medini, Duccio and Riley, David R and Tettelin, Hervé
Current Opinion in Microbiology, ISSN 1369-5274, 2014, Volume 23, pp. 148 - 154
Highlights • Next generation sequencing technologies have enabled large-scale genome analyses. • Pan-genome analyses provide a framework for predicting and... 
Pathology | STRAINS | CORE | STREPTOCOCCUS-PNEUMONIAE | EVOLUTION | NEISSERIA-MENINGITIDIS | ESCHERICHIA-COLI | SEQUENCE | MICROBIOLOGY | PANGENOME | SUPRAGENOME | MULTIPLE ALIGNMENT | Sequence Alignment - methods | Computational Biology - methods | Animals | Humans | Computational Biology - trends | Genomics - methods | Genomics - trends | Genome, Microbial | Genetic research | Analysis | Genomics
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5. Full Text Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
by Ming, Ray and VanBuren, Robert and Liu, Yanling and Yang, Mei and Han, Yuepeng and Li, Lei-Ting and Zhang, Qiong and Kim, Min-Jeong and Schatz, Michael C and Campbell, Michael and Li, Jingping and Bowers, John E and Tang, Haibao and Lyons, Eric and Ferguson, Ann A and Narzisi, Giuseppe and Nelson, David R and Blaby-Haas, Crysten E and Gschwend, Andrea R and Jiao, Yuannian and Der, Joshua P and Zeng, Fanchang and Han, Jennifer and Min, Xiang Jia and Hudson, Karen A and Singh, Ratnesh and Grennan, Aleel K and Karpowicz, Steven J and Watling, Jennifer R and Ito, Kikukatsu and Robinson, Sharon A and Hudson, Matthew E and Yu, Qingyi and Mockler, Todd C and Carroll, Andrew and Zheng, Yun and Sunkar, Ramanjulu and Jia, Ruizong and Chen, Nancy and Arro, Jie and Wai, Ching Man and Wafula, Eric and Spence, Ashley and Han, Yanni and Xu, Liming and Zhang, Jisen and Peery, Rhiannon and Haus, Miranda J and Xiong, Wenwei and Walsh, James A and Wu, Jun and Wang, Ming-Li and Zhu, Yun J and Paull, Robert E and Britt, Anne B and Du, Chunguang and Downie, Stephen R and Schuler, Mary A and Michael, Todd P and Long, Steve P and Ort, Donald R and William Schopf, J and Gang, David R and Jiang, Ning and Yandell, Mark and dePamphilis, Claude W and Merchant, Sabeeha S and Paterson, Andrew H and Buchanan, Bob B and Li, Shaohua and Shen-Miller, Jane
Genome Biology, ISSN 1474-7596, 2013, Volume 14, Issue 5, pp. R41 - R41
Background: Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago,... 
FRUITS | RATES | EVOLUTION | EARLY DIVERSIFICATION | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SEQUENCE | GENETICS & HEREDITY | CORE EUDICOTS | PLANTS | DIVERGENCE TIMES | PALEOHEXAPLOIDY | Nelumbo - physiology | Adaptation, Biological | Molecular Sequence Data | Nelumbo - classification | Mutation Rate | Genome, Plant | Phylogeny | Vitis - genetics | Amino Acid Substitution | Evolution, Molecular | Nelumbo - genetics | Research
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6. Full Text Dynamics of Pseudomonas aeruginosa Genome Evolution
by Kalai Mathee and Giri Narasimhan and Camilo Valdes and Xiaoyun Qiu and Jody M. Matewish and Michael Koehrsen and Antonis Rokas and Chandri N. Yandava and Reinhard Engels and Erliang Zeng and Raquel Olavarietta and Melissa Doud and Roger S. Smith and Philip Montgomery and Jared R. White and Paul A. Godfrey and Chinnappa Kodira and Bruce Birren and James E. Galagan and Stephen Lory
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 2/2008, Volume 105, Issue 8, pp. 3100 - 3105
One of the hallmarks of the Gram-negative bacterium Pseudomonas aeruginosa is its ability to thrive in diverse environments that includes humans with a variety... 
Genes | Genomics | Evolution | Pseudomonas aeruginosa | Evolutionary genetics | Cystic fibrosis | Genomes | Infections | Open reading frames | Chromosomes | Comparative genomics | Core and accessory genomes | Horizontal gene transfer | BACTERIA | INFECTIONS | BIAS | MULTIDISCIPLINARY SCIENCES | core and accessory genomes | LIBRARY | VIRULENCE | horizontal gene transfer | comparative genomics | CLONE | CYSTIC-FIBROSIS PATIENTS | ESSENTIALITY | HABITATS | STRAIN | Genome, Bacterial | Pseudomonas Infections - etiology | Humans | Molecular Sequence Data | Phylogeny | Cystic Fibrosis - complications | Pseudomonas Infections - microbiology | Sequence Analysis, DNA | Sequence Alignment | Pseudomonas aeruginosa - genetics | Base Sequence | Environment | Evolution, Molecular | Genetic aspects | Biological Sciences
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7. Full Text PGAP: pan-genomes analysis pipeline
by Zhao, Yongbing and Wu, Jiayan and Yang, Junhui and Sun, Shixiang and Xiao, Jingfa and Yu, Jun
Bioinformatics, ISSN 1367-4803, 2/2012, Volume 28, Issue 3, pp. 416 - 418
With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information... 
CORE | EVOLUTION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | INSIGHTS | Streptococcus pyogenes - genetics | Genome, Bacterial | Software | Algorithms | Streptococcus pyogenes - classification | Applications Note
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8. Full Text The DNA-encoded nucleosome organization of a eukaryotic genome
by Kaplan, Noam and Moore, Irene K and Fondufe-Mittendorf, Yvonne and Gossett, Andrea J and Tillo, Desiree and Field, Yair and LeProust, Emily M and Hughes, Timothy R and Lieb, Jason D and Widom, Jonathan and Segal, Eran
Nature, ISSN 0028-0836, 03/2009, Volume 458, Issue 7236, pp. 362 - 366
Nucleosome organization is critical for gene regulation(1). In living cells this organization is determined by multiple factors, including the action of... 
CORE | PROMOTER ELEMENT | MULTIDISCIPLINARY SCIENCES | HIGH-RESOLUTION | SEQUENCE | TRANSCRIPTION | SITES | SACCHAROMYCES-CEREVISIAE | YEAST GENOME | MULTIPLE ALIGNMENT | HISTONE | Caenorhabditis elegans - genetics | Saccharomyces cerevisiae - genetics | RNA, Messenger - genetics | Computational Biology | Nucleosomes - metabolism | Eukaryotic Cells - metabolism | Nucleosomes - genetics | RNA, Messenger - metabolism | Sequence Analysis, DNA | Transcription Factors - metabolism | Animals | Genome, Fungal - genetics | Micrococcal Nuclease - metabolism | Base Sequence | Chickens | Computer Simulation | Saccharomyces cerevisiae - growth & development | Eukaryotes | Usage | Nucleotide sequence | Nucleosomes | Genetic aspects | Nucleotide sequencing | Structure | Properties | Genetics | Maps | Chromosomes | Genes | Deoxyribonucleic acid--DNA
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9. Full Text High-Resolution Mapping and Characterization of Open Chromatin across the Genome
by Boyle, Alan P and Davis, Sean and Shulha, Hennady P and Meltzer, Paul and Margulies, Elliott H and Weng, Zhiping and Furey, Terrence S and Crawford, Gregory E
Cell, ISSN 0092-8674, 2008, Volume 132, Issue 2, pp. 311 - 322
Mapping DNase I hypersensitive (HS) sites is an accurate method of identifying the location of genetic regulatory elements, including promoters, enhancers,... 
DNA | NUCLEOSOME CORE | INTERFERON-GAMMA | GENE | PROTEIN CTCF | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSCRIPTION | BINDING SITES | ENHANCER | IDENTIFICATION | REGULATORY ELEMENTS | DNASE HYPERSENSITIVE SITES | CELL BIOLOGY | Promoter Regions, Genetic | Oligonucleotide Array Sequence Analysis | Area Under Curve | Histones - chemistry | Nucleosomes - chemistry | CD4-Positive T-Lymphocytes - cytology | Humans | Sequence Analysis, DNA | Genome, Human - genetics | Transcription Factors - metabolism | Algorithms | Cell Nucleus - metabolism | Chromatin Immunoprecipitation | Deoxyribonuclease I - chemistry | Deoxyribonuclease I - pharmacology | Chromosome Mapping - methods | Sensitivity and Specificity | ROC Curve | Chromosomes, Human | Binding Sites | Chromatin - genetics | Genome, Human - immunology | Genetic research | Chromatin | Genetic aspects | Genomics
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10. Full Text HUPAN: a pan-genome analysis pipeline for human genomes
by Duan, ZQ and Qiao, YY and Lu, JY and Lu, HM and Zhang, WM and Yan, FZ and Sun, C and Hu, ZQ and Zhang, Z and Li, GC and Chen, HZ and Xiang, Z and Zhu, ZG and Zhao, HY and Yu, YY and Wei, CC
GENOME BIOLOGY, ISSN 1474-760X, 07/2019, Volume 20, Issue 1, pp. 149 - 11
The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions.... 
Population-specific variation | READ ALIGNMENT | Pan-genome | Core genome | Presence-absence variation (PAV) | CHIMPANZEE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ANNOTATION | SEQUENCE | GENETICS & HEREDITY | DIVERSITY | Genome assembly | INSIGHTS
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11. Full Text How the fanconi anemia pathway guards the genome
by Moldovan, George-Lucian and D'Andrea, Alan D
Annual Review of Genetics, ISSN 0066-4197, 12/2009, Volume 43, Issue 1, pp. 223 - 249
Fanconi Anemia (FA) is an inherited genomic instability disorder, caused by mutations in genes regulating replication-dependent removal of interstrand DTNA... 
Interstrand crosslink | DNA repair | Translesion synthesis | Homologous recombination | Cancer | Protein ubiquitination | MONOUBIQUITINATED FANCD2 | interstrand crosslink | FUNCTIONAL-RELATIONSHIPS | protein ubiquitination | DNA-DAMAGE | CORE COMPLEX | NUCLEOTIDE EXCISION-REPAIR | PROTEIN COMPLEX | NUCLEAR ACCUMULATION | TARGETED DISRUPTION | homologous recombination | CROSS-LINK REPAIR | GENETICS & HEREDITY | cancer | translesion synthesis | Fanconi Anemia Complementation Group Proteins - metabolism | Animals | Metabolic Networks and Pathways | Genome | DNA Repair | Humans | Genetic aspects | Genetic recombination | Ubiquitin-proteasome system | Analysis | Fanconi's anemia | Index Medicus
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