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1. Full Text Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
by Hillier, L.W and Miller, W and Birney, E and Groenen, M.A.M and Crooijmans, R.P.M.A and Aerts, J and Poel, van der, J.J and International Chicken Genome Sequencing Consortium and Medicinska fakulteten and Medicinska och farmaceutiska vetenskapsområdet and Institutionen för medicinsk biokemi och mikrobiologi and Evolutionsbiologi and Institutionen för evolution, genomik och systematik and Teknisk-naturvetenskapliga vetenskapsområdet and Biologiska sektionen and Uppsala universitet
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... 
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 | 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
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2. Full Text Accounting for alignment uncertainty in phylogenomics
by Wu, Martin and Chatterji, Sourav and Eisen, Jonathan A
PLoS ONE, ISSN 1932-6203, 01/2012, Volume 7, Issue 1, p. e30288
Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions... 
MAXIMUM-LIKELIHOOD | POSITIONS | BLOCKS | MOLECULAR EVOLUTION | ALGORITHM | BIOLOGY | IMPROVEMENT | TREE | SELECTION | MULTIPLE SEQUENCE ALIGNMENT | PHYLOGENETIC INFERENCE | Amino Acid Sequence | Sequence Alignment - methods | Computational Biology - methods | Reproducibility of Results | Uncertainty | Algorithms | Animals | Humans | Software | Phylogeny | Genomics - methods | Evolution, Molecular | Analysis | Encyclopedias | Amino acid sequence | Genomes | Impact analysis | Proteins | Alignment | Simulation | Quality | Phylogenetics | Evolution | Masking | Trends | Bioinformatics | Methods
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3. Full Text Assembling the marine metagenome, one cell at a time
by Woyke, Tanja and Xie, Gary and Copeland, Alex and González, José M and Han, Cliff and Kiss, Hajnalka and Saw, Jimmy H and Senin, Pavel and Yang, Chi and Chatterji, Sourav and Cheng, Jan-Fang and Eisen, Jonathan A and Sieracki, Michael E and Stepanauskas, Ramunas and Joint Genome Institute (JGI)
PLoS ONE, ISSN 1932-6203, 04/2009, Volume 4, Issue 4, pp. e5299 - e5299
The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human... 
BIOLOGY | RNA, Ribosomal, 16S - metabolism | Genome, Bacterial | Genes, Bacterial - genetics | Rhodopsins, Microbial | Phylogeny | Biodiversity | Sequence Analysis, DNA | Marine Biology | Animals | Rhodopsin - genetics | Plankton | RNA, Ribosomal, 16S - genetics | Genomics - methods | Analysis | Genes | Genomics | Force and energy | Genomes | Nucleotide sequencing | Niche (Ecology) | DNA sequencing | Adaptations | Peptides | Nucleotides | Gene sequencing | Complexity | Taxa | Microorganisms | Bioinformatics | Deoxyribonucleic acid--DNA | Transfer RNA | Potential energy | Enzymes | Cultivation | Metabolism | Ocean surface | Quality control | Comparative analysis | Niches | Flow cytometry | Laboratories | Fluorescence | Biogeography | Energy sources | Identification | Biopolymers | Bacterioplankton | Oxidation | Localization | Strains (organisms) | Ocean currents | Geographical distribution | Reconstruction | Biodegradation | Bacterial proteins | Cloning | Nuclear electric power generation | Abundance | Marine microorganisms | Algorithms | Ecological niches | Contaminants | Genetic testing | Molecular biology | Pollutant removal | Deoxyribonucleic acid | DNA
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4. Full Text Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum
by Wu, Dongying and Raymond, Jason and Wu, Martin and Chatterji, Sourav and Ren, Qinghu and Graham, Joel E and Bryant, Donald A and Robb, Frank and Colman, Albert and Tallon, Luke J and Badger, Jonathan H and Madupu, Ramana and Ward, Naomi L and Eisen, Jonathan A and Joint Genome Institute (JGI)
PLoS ONE, ISSN 1932-6203, 01/2009, Volume 4, Issue 1, p. e4207
In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an "Assembling the Tree of Life" project,... 
BIOLOGY | Hot Springs - microbiology | Chloroflexi - classification | Gram-Negative Bacteria | Phylogeny | Carbon Monoxide - metabolism | Chemotaxis - genetics | Sequence Analysis, DNA | Genome, Bacterial - genetics | Chloroflexi - genetics | Metabolic Networks and Pathways | DNA, Circular | Bacteria, Aerobic | Flagella - genetics | Photosynthesis | Carotenoids | RNA | Analysis | Phytochemistry | Genes | Genomics | Genetic aspects | Genomes | Circular DNA | Hot springs | Biological evolution | Biochemistry | Chemoreception | Data bases | Water springs | Proteins | National parks | Phylogenetics | Bacteria | International conferences | Oxidation | Chromosomes | Diols | Deoxyribonucleic acid--DNA | Enzymes | Nucleotide sequence | Cell walls | rRNA | Glycosylation | Metabolism | Chemotaxis | Algorithms | Insects | Molecular biology | Flagella | Deoxyribonucleic acid | DNA
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5. Full Text Genome sequence of the Brown Norway rat yields insights into mammalian evolution
by Gibbs, Richard A and Weinstock, George M and Metzker, Michael L and Muzny, Donna M and Sodergren, Erica J and Scherer, Steven and Scott, Graham and Steffen, David and Worley, Kim C and Burch, Paula E and Okwuonu, Geoffrey and Hines, Sandra and Lewis, Lora and Deramo, Christine and Delgado, Oliver and Dugan-Rocha, Shannon and Miner, George and Morgan, Margaret and Hawes, Alicia and Gill, Rachel and Holt, Robert A and Adams, Mark D and Amanatides, Peter G and Baden-Tillson, Holly and Barnstead, Mary and Chin, Soo and Evans, Cheryl A and Ferriera, Steve and Fosler, Carl and Glodek, Anna and Gu, Zhiping and Jennings, Don and Kraft, Cheryl L and Nguyen, Trixie and Pfannkoch, Cynthia M and Sitter, Cynthia and Sutton, Granger G and Venter, J. Craig and Woodage, Trevor and Smith, Douglas and Lee, Hong-Mei and Gustafson, Erik and Cahill, Patrick and Kana, Arnold and Doucette-Stamm, Lynn and Weinstock, Keith and Fechtel, Kim and Weiss, Robert B and Dunn, Diane M and Green, Eric D and Blakesley, Robert W and Bouffard, Gerard G and de Jong, Pieter J and Osoegawa, Kazutoyo and Zhu, Baoli and Marra, Marco and Schein, Jacqueline and Bosdet, Ian and Fjell, Chris and Jones, Steven and Krzywinski, Martin and Mathewson, Carrie and Siddiqui, Asim and Wye, Natasja and McPherson, John and Zhao, Shaying and Fraser, Claire M and Shetty, Jyoti and Shatsman, Sofiya and Geer, Keita and Chen, Yixin and Abramzon, Sofyia and Nierman, William C and Gibbs, Richard A and Weinstock, George M and Havlak, Paul H and Chen, Rui and Durbin, K. James and Egan, Amy and Ren, Yanru and Song, Xing-Zhi and Li, Bingshan and Liu, Yue and Qin, Xiang and Cawley, Simon and Weinstock, George M and Worley, Kim C and Cooney, A.J and Gibbs, Richard A and D'Souza, Lisa M and Martin, Kirt and Wu, Jia Qian and Gonzalez-Garay, Manuel L and Jackson, Andrew R and Kalafus, Kenneth J and McLeod, Michael P and Milosavljevic, Aleksandar and Virk, Davinder and Volkov, Andrei and Wheeler, David A and ... and Rat Genome Sequencing Project Cons and Rat Genome Sequencing Project Consortium and Joint Genome Institute (JGI) and Naturvetenskapliga fakulteten and Department of Mathematical Statistics and Institutionen för matematisk statistik and Faculty of Sciences and Göteborgs universitet and Gothenburg University
Nature, ISSN 0028-0836, 04/2004, Volume 428, Issue 6982, pp. 493 - 521
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human... 
MAJOR URINARY PROTEINS | ARTIFICIAL CHROMOSOME LIBRARY | LOCUS-CONTROL REGION | MOUSE GENOME | DNA-SEQUENCE | MULTIDISCIPLINARY SCIENCES | RECENT SEGMENTAL DUPLICATIONS | ANIMAL-MODEL | GENE PREDICTION | MURINE ENDOGENOUS RETROVIRUS | EMBRYONIC EPSILON-GLOBIN | Gene Duplication | Rats, Inbred BN - genetics | Chromosomes, Mammalian - genetics | Genomics | Humans | Male | RNA, Untranslated - genetics | Retroelements - genetics | DNA, Mitochondrial - genetics | DNA Transposable Elements - genetics | Telomere - genetics | Introns - genetics | RNA Splice Sites - genetics | Models, Molecular | Rats | Sequence Analysis, DNA | Regulatory Sequences, Nucleic Acid - genetics | Animals | Mutagenesis | Base Composition | Centromere - genetics | CpG Islands - genetics | Polymorphism, Single Nucleotide - genetics | Mice | Genome | Evolution, Molecular | Medical research | Evolution | Disease | Comparative analysis | Rodents | Genetik | Biokemi och molekylärbiologi | Biochemistry and Molecular Biology | Genetics | Cellbiologi | Sannolikhetsteori och statistik | Bioinformatik och systembiologi | Bioinformatics and Systems Biology | Probability Theory and Statistics | Cell Biology
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6. Full Text In vitro and in silico studies on fibrinolytic activity of nattokinase： A clot buster from Bacillus sp
by V. Mohanasrinivasan. A. Mohanapriya Swaroop Potdar Sourav Chatterji Srinath Konne Sweta Kumari S. Merlyn Keziah. C. Subathra Devi
生物学前沿：英文版, ISSN 1674-7984, 2017, Volume 12, Issue 3, pp. 219 - 225
BACKGROUND： Nattokinase （NK） is a serine protease enzyme of the subtilisin family. It exhibits a strong fibrinolytic activity. The fibrinolytic enzymes from... 
纤溶活性 | SDS-PAGE | 枯草杆菌蛋白酶 | Bacillus | 纤维蛋白原 | 纳豆激酶 | 氨基酸残基 | 活性硅 | docking | clot busters | Bacillus sp | nattokinase (NK) | Fibrin | Casein | Proteases | Analysis | Fibrinogen | Molecular dynamics | Gardens
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7. Full Text Evolution of genes and genomes on the Drosophila phylogeny
by Clark, Andrew G and Eisen, Michael B and Smith, Douglas R and Bergman, Casey M and Oliver, Brian and Markow, Therese A and Kaufman, Thomas C and Kellis, Manolis and Gelbart, William and Iyer, Venky N and Pollard, Daniel A and Sackton, Timothy B and Larracuente, Amanda M and Singh, Nadia D and Abad, Jose P and Abt, Dawn N and Adryan, Boris and Aguade, Montserrat and Akashi, Hiroshi and Anderson, Wyatt W and Aquadro, Charles F and Ardell, David H and Arguello, Roman and Artieri, Carlo G and Barbash, Daniel A and Barker, Daniel and Barsanti, Paolo and Batterham, Phil and Batzoglou, Serafim and Begun, Dave and Bhutkar, Arjun and Blanco, Enrico and Bosak, Stephanie A and Bradley, Robert K and Brand, Adrianne D and Brent, Michael R and Brooks, Angela N and Brown, Randall H and Butlin, Roger K and Caggese, Corrado and Calvi, Brian R and Bernardo De Carvalho, A and Caspi, Anat and Castrezana, Sergio and Celniker, Susan E and Chang, Jean L and Chapple, Charles and Chatterji, Sourav and Chinwalla, Asif and Civetta, Alberto and Clifton, Sandra W and Comeron, Josep M and Costello, James C and Coyne, Jerry A and Daub, Jennifer and David, Robert G and Delcher, Arthur L and Delehaunty, Kim and Do, Chuong B and Ebling, Heather and Edwards, Kevin and Eickbush, Thomas and Evans, Jay D and Filipski, Alan and Findeiß, Sven and Freyhult, Eva and Fulton, Lucinda and Fulton, Robert and Garcia, Ana C. L and Gardiner, Anastasia and Garfield, David A and Garvin, Barry E and Gibson, Greg and Gilbert, Don and Gnerre, Sante and Godfrey, Jennifer and Good, Robert and Gotea, Valer and Gravely, Brenton and Greenberg, Anthony J and Griffiths-Jones, Sam and Gross, Samuel and Guigo, Roderic and Gustafson, Erik A and Haerty, Wilfried and Hahn, Matthew W and Halligan, Daniel L and Halpern, Aaron L and Halter, Gillian M and Han, Mira V and Heger, Andreas and Hillier, LaDeana and Hinrichs, Angie S and Holmes, Ian and Hoskins, Roger A and Hubisz, Melissa J and Hultmark, Dan and Huntley, Melanie A and Jaffe, David B and Jagadeeshan, Santosh and ... and Drosophila 12 Genomes Consor and Broad Inst Whole Genome Ass and Broad Inst Genome Sequencing and Drosophila 12 Genomes Consortium and Medicinska fakulteten and Umeå centrum för molekylär patogenes (UCMP) (Medicinska fakulteten) and Umeå universitet
Nature, ISSN 0028-0836, 11/2007, Volume 450, Issue 7167, pp. 203 - 218
Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing... 
SYNONYMOUS CODON USAGE | ADAPTIVE PROTEIN EVOLUTION | NONCODING DNA | FRUIT-FLY | MULTIDISCIPLINARY SCIENCES | MOLECULAR EVOLUTION | NATURAL-SELECTION | HOST-DEFENSE | MITOCHONDRIAL-DNA | FAMILY EVOLUTION | AMINO-ACID SUBSTITUTION | Multigene Family - genetics | Synteny - genetics | Genes, Insect - genetics | Genomics | Genome, Insect - genetics | Genome, Mitochondrial - genetics | Reproduction - genetics | Drosophila - classification | Phylogeny | RNA, Untranslated - genetics | Sequence Analysis, DNA | Gene Order - genetics | Sequence Alignment | Animals | DNA Transposable Elements - genetics | Drosophila - immunology | Codon - genetics | Drosophila - metabolism | Drosophila Proteins - genetics | Immunity - genetics | Drosophila - genetics | Evolution, Molecular | Comparative studies | Evolution |