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Environmental microbiology, ISSN 1462-2912, 07/2019
Negativicutes are Gram-Negative bacteria characterized by two cell membranes, but they are phylogenetically a side-branch of Gram-Positive Firmicutes that... 
Journal Article
Bioinformatics, ISSN 1367-4803, 05/2010, Volume 26, Issue 13, pp. 1669 - 1670
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 12/2012, Volume 40, Issue 22, pp. 11673 - 11683
Journal Article
Bioinformatics, ISSN 1367-4803, 10/2015, Volume 31, Issue 19, pp. 3210 - 3212
Motivation: Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly... 
QUALITY | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | TOOL | Gene Dosage - genetics | Computational Biology - methods | Animals | Humans | Molecular Sequence Annotation - methods | Software | Genome | Genomics - methods | Annotations | Completeness | Genomes | Assessments | Bioinformatics | Assembly | Computer programs
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 1/2008, Volume 36, Issue suppl_1, pp. D271 - D275
The concept of orthology is widely used to relate genes across different species using comparative genomics, and it provides the basis for inferring gene... 
PROTEIN | DATABASE | BLOCKS | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENOME | GENES | User-Computer Interface | Animals | Vertebrates - genetics | Genomics | Proteomics | Databases, Genetic | Internet | Phylogeny | Insecta - genetics | Fungi - genetics
Journal Article
Methods in molecular biology (Clifton, N.J.), 2019, Volume 1962, p. 227
Genomics drives the current progress in molecular biology, generating unprecedented volumes of data. The scientific value of these sequences depends on the... 
Markov Chains | Transcriptome | Databases, Genetic | Gene Dosage | Molecular Sequence Annotation - methods | Software | Internet | Genome | Genomics - methods
Journal Article
Molecular Biology and Evolution, ISSN 0737-4038, 2018, Volume 35, Issue 3, pp. 543 - 548
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of... 
Metagenomics | Evolution | Transcriptomics | Bioinformatics | PLANT | EVOLUTIONARY | ORTHOLOGS | BIOCHEMISTRY & MOLECULAR BIOLOGY | COMPLETENESS | evolution | BACTERIAL | ORTHODB | GENOME | EVOLUTIONARY BIOLOGY | metagenomics | FUNGAL | bioinformatics | GENETICS & HEREDITY | transcriptomics | IMPROVEMENTS | TOOL | Fast Track
Journal Article
Nucleic acids research, ISSN 0305-1048, 2013, Volume 41, Issue W1, pp. W165 - 168
MicroRNAs (miRNAs) posttranscriptionally repress the expression of protein-coding genes. Based on the partial complementarity between miRNA and messenger RNA... 
RECOGNITION | BIOCHEMISTRY & MOLECULAR BIOLOGY | ACCESSIBILITY | Thermodynamics | Sequence Analysis, RNA | Gene Expression Regulation | MicroRNAs - metabolism | RNA, Messenger - chemistry | Software | Internet | 3' Untranslated Regions | RNA, Messenger - metabolism | MicroRNAs - chemistry
Journal Article
Nature, ISSN 0028-0836, 2004, Volume 432, Issue 7018, pp. 695 - 716
We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first... 
MOUSE GENOME | NON-LTR RETROTRANSPOSONS | ALCOHOL-DEHYDROGENASE | PHYLOGENETIC ANALYSIS | MULTIDISCIPLINARY SCIENCES | BROWN-NORWAY RAT | RECENT SEGMENTAL DUPLICATIONS | MAJOR HISTOCOMPATIBILITY COMPLEX | TISSUE-SPECIFIC GENES | OLFACTORY RECEPTOR | MAMMALIAN EVOLUTION | Gene Duplication | Multigene Family - genetics | Conserved Sequence - genetics | Vertebrates - genetics | Physical Chromosome Mapping | Genomics | Humans | Long Interspersed Nucleotide Elements - genetics | Mutagenesis - genetics | Synteny | Genes - genetics | Short Interspersed Nucleotide Elements - genetics | RNA, Untranslated - genetics | Sequence Analysis, DNA | Pseudogenes - genetics | Animals | Retroviridae - genetics | DNA Transposable Elements - genetics | Chickens - genetics | Genome | Avian Proteins - genetics | Evolution, Molecular | Birds | Evolution | Genetic diversity | Gene expression | Mammals | Chromosomes | Research Support; U.S. Gov't; P.H.S | Research Support; U.S. Gov't; Non-P.H.S | Comparative Study | Long Interspersed Nucleotide Elements/genetics | Biology | Avian Proteins/genetics | Vertebrates/genetics | Short Interspersed Nucleotide Elements/genetics | Pseudogenes/genetics | Genetics | Research Support; Non-U.S. Gov't | Biologi | Natural Sciences | Biological Sciences | RNA; Untranslated/genetics | Mutagenesis/genetics | DNA Transposable Elements/genetics | Multigene Family/genetics | Retroviridae/genetics | Sequence Analysis; DNA | Genetik | Genes/genetics | Naturvetenskap | Conserved Sequence/genetics | Evolution; Molecular | Biologiska vetenskaper | Cell and molecular biology | Chickens/genetics | Cell- och molekylärbiologi | phylogenetic analysis | mammalian evolution | tissue-specific genes | brown-norway rat | non-ltr retrotransposons | major histocompatibility complex | olfactory receptor | mouse genome | recent segmental duplications | alcohol-dehydrogenase
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 01/2013, Volume 41, Issue 1, pp. D358 - D365
The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolution, and thus forms the cornerstone of comparative genomics,... 
PROTEIN | DATABASE | COMPARATIVE GENOMICS | EUKARYOTIC ORTHOLOGS | ENHANCEMENTS | INFORMATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | CULEX-QUINQUEFASCIATUS | PHYLOGENETIC TREES | RESOURCE | PROKARYOTES | Genes, Bacterial | Genes | Humans | Molecular Sequence Annotation | Synteny | Databases, Genetic | Phylogeny | Phenotype | Animals | Genes, Fungal | Mice | Internet | Cluster Analysis | Evolution, Molecular
Journal Article
American Journal of Human Genetics, ISSN 0002-9297, 12/2014, Volume 95, Issue 6, p. 660
  Gene expression levels can be subject to selection. We hypothesized that the age of gene origin is associated with expression constraints, given that it... 
Human subjects | Biological variation | Genes | Evolution | Genomes | Gene expression
Journal Article
by Gulia-Nuss, Monika and Nuss, Andrew B and Meyer, Jason M and Sonenshine, Daniel E and Roe, R. Michael and Waterhouse, Robert M and Sattelle, David B and De La Fuente, José and Ribeiro, Jose M and Megy, Karine and Thimmapuram, Jyothi and Miller, Jason R and Walenz, Brian P and Koren, Sergey and Hostetler, Jessica B and Thiagarajan, Mathangi and Joardar, Vinita S and Hannick, Linda I and Bidwell, Shelby and Hammond, Martin P and Young, Sarah and Zeng, Qiandong and Abrudan, Jenica L and Almeida, Francisca C and Ayllón, Nieves and Bhide, Ketaki and Bissinger, Brooke W and Bonzon-Kulichenko, Elena and Buckingham, Steven D and Caffrey, Daniel R and Caimano, Melissa J and Croset, Vincent and Driscoll, Timothy and Gilbert, Don and Gillespie, Joseph J and Giraldo-Calderón, Gloria I and Grabowski, Jeffrey M and Jiang, David and Khalil, Sayed M.S and Kim, Donghun and Kocan, Katherine M and Koči, Juraj and Kuhn, Richard J and Kurtti, Timothy J and Lees, Kristin and Lang, Emma G and Kennedy, Ryan C and Kwon, Hyeogsun and Perera, Rushika and Qi, Yumin and Radolf, Justin D and Sakamoto, Joyce M and Sánchez-Gracia, Alejandro and Severo, Maiara S and Silverman, Neal and Šimo, Ladislav and Tojo, Marta and Tornador, Cristian and Van Zee, Janice P and Vázquez, Jesús and Vieira, Filipe G and Villar, Margarita and Wespiser, Adam R and Yang, Yunlong and Zhu, Jiwei and Arensburger, Peter and Pietrantonio, Patricia V and Barker, Stephen C and Shao, Renfu and Zdobnov, Evgeny M and Hauser, Frank and Grimmelikhuijzen, Cornelis J.P and Park, Yoonseong and Rozas, Julio and Benton, Richard and Pedra, Joao H.F and Nelson, David R and Unger, Maria F and Tubio, Jose M.C and Tu, Zhijian and Robertson, Hugh M and Shumway, Martin and Sutton, Granger and Wortman, Jennifer R and Lawson, Daniel and Wikel, Stephen K and Nene, Vishvanath M and Fraser, Claire M and Collins, Frank H and Birren, Bruce and Nelson, Karen E and Caler, Elisabet and Hill, Catherine A
Nature Communications, ISSN 2041-1723, 02/2016, Volume 7, Issue 1, p. 10507
Journal Article