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1. Full Text BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs
by Simão, Felipe A and Waterhouse, Robert M and Ioannidis, Panagiotis and Kriventseva, Evgenia V and Zdobnov, Evgeny M
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
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2. Full Text OrthoDB: the hierarchical catalog of eukaryotic orthologs
by Kriventseva, Evgenia V and Rahman, Nazim and Espinosa, Octavio and Zdobnov, Evgeny M
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
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3. Full Text OrthoDB v9.1: Cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs
by Zdobnov, Evgeny M and Tegenfeldt, Fredrik and Kuznetsov, Dmitry and Waterhouse, Robert M and Simao, Felipe A and Ioannidis, Panagiotis and Seppey, Mathieu and Loetscher, Alexis and Kriventseva, Evgenia V
Nucleic Acids Research, ISSN 0305-1048, 01/2017, Volume 45, Issue 1, pp. D744 - D749
OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached... 
HIERARCHICAL CATALOG | DATABASE | GENE | INFORMATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | RESOURCE | User-Computer Interface | Computational Biology - methods | Viruses - genetics | Molecular Sequence Annotation | Databases, Genetic | Bacteria - genetics | Fungi - genetics | Algorithms | Animals | Plants - genetics | Archaea - genetics | Software | Genomics - methods | Web Browser | Evolution, Molecular | Database Issue
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4. Full Text BUSCO applications from quality assessments to gene prediction and phylogenomics
by Waterhouse, Robert M and Seppey, Mathieu and Simao, Felipe A and Manni, Mosè and Ioannidis, Panagiotis and Klioutchnikov, Guennadi and Kriventseva, Evgenia V and Zdobnov, Evgeny M
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
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5. Full Text OrthoDB: A hierarchical catalog of animal, fungal and bacterial orthologs
by Waterhouse, Robert M and Tegenfeldt, Fredrik and Li, Jia and Zdobnov, Evgeny M and Kriventseva, Evgenia V
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
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6. Full Text OrthoDB v8: Update of the hierarchical catalog of orthologs and the underlying free software
by Kriventseva, Evgenia V and Tegenfeldt, Fredrik and Petty, Tom J and Waterhouse, Robert M and Simão, Felipe A and Pozdnyakov, Igor A and Ioannidis, Panagiotis and Zdobnov, Evgeny M
Nucleic Acids Research, ISSN 0305-1048, 01/2015, Volume 43, Issue 1, pp. D250 - D256
Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data,... 
PROTEIN | GENOME DATABASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | ACCESS | ALGORITHM | RESOURCE | Sequence Homology | Algorithms | Animals | Eukaryota - genetics | Data Curation | Humans | Databases, Genetic | Software | Evolution, Molecular | Genome, Microbial | Database Issue
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7. Full Text Genome Sequence of Aedes aegypti, a Major Arbovirus Vector
by Vishvanath Nene and Jennifer R. Wortman and Daniel Lawson and Brian Haas and Chinnappa Kodira and Zhijian (Jake) Tu and Brendan Loftus and Zhiyong Xi and Karyn Megy and Manfred Grabherr and Quinghu Ren and Evgeny M. Zdobnov and Neil F. Lobo and Kathryn S. Campbell and Susan E. Brown and Maria F. Bonaldo and Jingsong Zhu and Steven P. Sinkins and David G. Hogenkamp and Paolo Amedeo and Peter Arensburger and Peter W. Atkinson and Shelby Bidwell and Jim Biedler and Ewan Birney and Robert V. Bruggner and Javier Costas and Monique R. Coy and Jonathan Crabtree and Matt Crawford and Becky deBruyn and David DeCaprio and Karin Eiglmeier and Eric Eisenstadt and Hamza El-Dorry and William M. Gelbart and Suely L. Gomes and Martin Hammond and Linda I. Hannick and James R. Hogan and Michael H. Holmes and David Jaffe and J. Spencer Johnston and Ryan C. Kennedy and Hean Koo and Saul Kravitz and Evgenia V. Kriventseva and David Kulp and Kurt LaButti and Eduardo Lee and Song Li and Diane D. Lovin and Chunhong Mao and Evan Mauceli and Carlos F. M. Menck and Jason R. Miller and Philip Montgomery and Akio Mori and Ana L. Nascimento and Horacio F. Naveira and Chad Nusbaum and Sinéad O'Leary and Joshua Orvis and Mihaela Pertea and Hadi Quesneville and Kyanne R. Reidenbach and Yu-Hui Rogers and Charles W. Roth and Jennifer R. Schneider and Michael Schatz and Martin Shumway and Mario Stanke and Eric O. Stinson and Jose M. C. Tubio and Janice P. VanZee and Sergio Verjovski-Almeida and Doreen Werner and Owen White and Stefan Wyder and Qiandong Zeng and Qi Zhao and Yongmei Zhao and Catherine A. Hill and Alexander S. Raikhel and Marcelo B. Soares and Dennis L. Knudson and Norman H. Lee and James Galagan and Steven L. Salzberg and Ian T. Paulsen and George Dimopoulos and Frank H. Collins and Bruce Birren and Claire M. Fraser-Liggett and David W. Severson
Science, ISSN 0036-8075, 6/2007, Volume 316, Issue 5832, pp. 1718 - 1723
We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at ∼1376 million base pairs is about 5... 
Transposons | Genetic vectors | Introns | Genes | DNA | Genomes | Insect vectors | Chromosomes | Insect genetics | Mosquitos | Research Article | ORGANIZATION | EVOLUTION | YELLOW-FEVER MOSQUITO | DROSOPHILA-MELANOGASTER | MULTIDISCIPLINARY SCIENCES | SUPERFAMILY | INSECTS | ANOPHELES-GAMBIAE | RECEPTORS | EXPRESSION | TRANSPOSONS | Anopheles - metabolism | Multigene Family | Species Specificity | Anopheles - genetics | Humans | Synteny | Molecular Sequence Data | Male | Drosophila melanogaster - genetics | Insect Vectors - metabolism | Yellow Fever - transmission | Aedes - metabolism | Sex Determination Processes | Membrane Transport Proteins - genetics | Base Sequence | Female | Transcription, Genetic | Genome, Insect | Genes, Insect | Yellow Fever - prevention & control | Insect Proteins - genetics | Arboviruses | Protein Structure, Tertiary - genetics | Sex Characteristics | Aedes - genetics | Sequence Analysis, DNA | DNA Transposable Elements | Dengue - prevention & control | Animals | Insect Vectors - genetics | Dengue - transmission | Physiological aspects | Aedes albopictus | Genetic aspects | Health aspects | Aedes | Comparative studies | Viruses | Disease transmission | Insects | Epidemiology | Genomics | Life Sciences | Anopheles gambiae | Protein Structure, Tertiary | Insect Vectors | Dengue | Biochemistry, Molecular Biology | Sex Determination (Genetics) | Membrane Transport Proteins | Yellow Fever | Drosophila melanogaster | Insect Proteins
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8. OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
by Waterhouse, Robert M and Zdobnov, Evgeny M and Tegenfeldt, Fredrik and Li, Jia and Kriventseva, Evgenia V
Nucleic Acids Research, ISSN 1362-4962, 01/2011, Volume 39, pp. D283 - D288
The concept of homology drives speculation on a gene's function in any given species when its biological roles in other species are characterized. With... 
orthology | Radiation | Data processing | Evolutionary genetics | Homology | Genomes | Phylogeny | genealogy | Fungi | Databases | Evolution | Sampling | Catalogs
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9. Full Text Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle
by Ewen F. Kirkness and Brian J. Haas and Weilin Sun and Henk R. Braig and M. Alejandra Perotti and John M. Clark and Si Hyeock Lee and Hugh M. Robertson and Ryan C. Kennedy and Eran Elhaik and Daniel Gerlach and Evgenia V. Kriventseva and Christine G. Elsik and Dan Graur and Catherine A. Hill and Jan A. Veenstra and Brian Walenz and José Manuel C. Tubío and José M. C. Ribeiro and Julio Rozas and J. Spencer Johnston and Justin T. Reese and Aleksandar Popadic and Marta Tojo and Didier Raoult and David L. Reed and Yoshinori Tomoyasu and Emily Krause and Omprakash Mittapalli and Venu M. Margam and Hong-Mei Li and Jason M. Meyer and Reed M. Johnson and Jeanne Romero-Severson and Janice Pagel VanZee and David Alvarez-Ponce and Filipe G. Vieira and Montserrat Aguadé and Sara Guirao-Rico and Juan M. Anzola and Kyong S. Yoon and Joseph P. Strycharz and Maria F. Unger and Scott Christley and Neil F. Lobo and Manfredo J. Seufferheld and NaiKuan Wang and Gregory A. Dasch and Claudio J. Struchiner and Greg Madey and Linda I. Hannick and Shelby Bidwell and Vinita Joardar and Elisabet Caler and Renfu Shao and Stephen C. Barker and Stephen Cameron and Robert V. Bruggner and Allison Regier and Justin Johnson and Lakshmi Viswanathan and Terry R. Utterback and Granger G. Sutton and Daniel Lawson and Robert M. Waterhouse and J. Craig Venter and Robert L. Strausberg and May R. Berenbaum and Frank H. Collins and Evgeny M. Zdobnov and Barry R. Pittendrigh
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 7/2010, Volume 107, Issue 27, pp. 12168 - 12173
As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing... 
Endosymbionts | Genes | Humans | Drosophila | Evolution | Genomes | Lice | Insect genomes | Insect vectors | Chromosomes | Comparative genomics | Coevolution | Ectoparasite | APIS-MELLIFERA | PEDICULUS-HUMANUS | EPIDEMIC TYPHUS | SUCKING LICE PHTHIRAPTERA | DROSOPHILA-MELANOGASTER | INSECTICIDE RESISTANCE | MULTIDISCIPLINARY SCIENCES | MOLECULAR EVOLUTION | ANOPHELES-GAMBIAE | DNA-BINDING PROTEIN | HONEY-BEE | Symbiosis | Pediculus - microbiology | Genes, Bacterial - genetics | Genes, Insect - genetics | Genome, Insect - genetics | Enterobacteriaceae - genetics | Molecular Sequence Data | Sequence Analysis, DNA | Genome, Bacterial - genetics | Animals | Pediculus - genetics | Genomics - methods | Lice Infestations - parasitology | Genomics | Parasitism | Genetic aspects | Research | Nucleotide sequencing | Methods | Protein binding | Enzymes | Pathogens | Mitochondrial DNA | Vectors | Parasites | Odorants | Vitamins | Diets | Symbionts | Taste receptors | Mitochondria | DNA-binding protein | Plasmids | Trench fever | Epidemic typhus | miRNA | Relapsing fever | ectoparasite | Biological Sciences | coevolution | comparative genomics
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10. Full Text The ecoresponsive genome of Daphnia pulex
by Colbourne, John K and Pfrender, Michael E and Gilbert, Donald and Thomas, W. Kelley and Tucker, Abraham and Oakley, Todd H and Tokishita, Shinichi and Aerts, Andrea and Arnold, Georg J and Basu, Malay Kumar and Bauer, Darren J and Cáceres, Carla E and Carmel, Liran and Casola, Claudio and Choi, Jeong-Hyeon and Detter, John C and Dong, Qunfeng and Dusheyko, Serge and Eads, Brian D and Fröhlich, Thomas and Geiler-Samerotte, Kerry A and Gerlach, Daniel and Hatcher, Phil and Jogdeo, Sanjuro and Krijgsveld, Jeroen and Kriventseva, Evgenia V and Kültz, Dietmar and Laforsch, Christian and Lindquist, Erika and Lopez, Jacqueline and Manak, J. Robert and Muller, Jean and Pangilinan, Jasmyn and Patwardhan, Rupali P and Pitluck, Samuel and Pritham, Ellen J and Rechtsteiner, Andreas and Rho, Mina and Rogozin, Igor B and Sakarya, Onur and Salamov, Asaf and Schaack, Sarah and Shapiro, Harris and Shiga, Yasuhiro and Skalitzky, Courtney and Smith, Zachary and Souvorov, Alexander and Sung, Way and Tang, Zuojian and Tsuchiya, Dai and Tu, Hank and Vos, Harmjan and Wang, Mei and Wolf, Yuri I and Yamagata, Hideo and Yamada, Takuji and Ye, Yuzhen and Shaw, Joseph R and Andrews, Justen and Crease, Teresa J and Tang, Haixu and Lucas, Susan M and Robertson, Hugh M and Bork, Peer and Koonin, Eugene V and Zdobnov, Evgeny M and Grigoriev, Igor V and Lynch, Michael and Boore, Jeffrey L and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Science, ISSN 0036-8075, 02/2011, Volume 331, Issue 6017, pp. 555 - 561
We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a... 
CAENORHABDITIS-ELEGANS | EVOLUTION | EXPRESSION | MAGNA | DUPLICATE GENES | MULTIDISCIPLINARY SCIENCES | Adaptation, Physiological | Gene Duplication | Amino Acid Sequence | Gene Expression | Multigene Family | Daphnia - physiology | Genes | Molecular Sequence Annotation | Gene Expression Regulation | Molecular Sequence Data | Chromosome Mapping | Gene Expression Profiling | Phylogeny | Sequence Analysis, DNA | Gene Conversion | Metabolic Networks and Pathways - genetics | Animals | Base Sequence | Ecosystem | Environment | Genes, Duplicate | Genome | Daphnia - genetics | Evolution, Molecular | Analysis | Genomes | Ecoresponsive Daphnia pulex | BASIC BIOLOGICAL SCIENCES
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11. Full Text OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs
by Kriventseva, Evgenia V and Kuznetsov, Dmitry and Tegenfeldt, Fredrik and Manni, Mosè and Dias, Renata and Simão, Felipe A and Zdobnov, Evgeny M
Nucleic Acids Research, ISSN 0305-1048, 01/2019, Volume 47, Issue D1, pp. D807 - D811
Abstract OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up of the... 
UPDATE | HIERARCHICAL CATALOG | DATABASE | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | PREDICTION | Database Issue
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12. Full Text OrthoDB: The hierarchical catalog of eukaryotic orthologs in 2011
by Waterhouse, Robert M and Zdobnov, Evgeny M and Tegenfeldt, Fredrik and Li, Jia and Kriventseva, Evgenia V
Nucleic Acids Research, ISSN 0305-1048, 01/2011, Volume 39, Issue 1, pp. D283 - D288
The concept of homology drives speculation on a gene's function in any given species when its biological roles in other species are characterized. With... 
EVOLUTIONARY | GENOME DATABASE | ANNOTATION | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | GENES | V2.0 | PHYLOGENETIC TREES | RESOURCE | INSIGHTS | Protein Structure, Tertiary | Arthropods - genetics | Vertebrates - genetics | Saccharomyces cerevisiae - genetics | Genes | Genomics | Molecular Sequence Annotation | Databases, Genetic | Phylogeny | Drosophila melanogaster - genetics | Fungi - genetics | Proteins - genetics | Sequence Homology, Amino Acid | Animals | Mice | Evolution, Molecular
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13. Full Text The common marmoset genome provides insight into primate biology and evolution
by Worley, Kim C and Warren, Wesley C and Rogers, Jeffrey and Locke, Devin and Muzny, Donna M and Mardis, Elaine R and Weinstock, George M and Tardif, Suzette D and Aagaard, Kjersti M and Archidiacono, Nicoletta and Arul Rayan, Nirmala and Batzer, Mark A and Beal, Kathryn and Brejova, Brona and Capozzi, Oronzo and Capuano, Saverio B and Casola, Claudio and Chandrabose, Mimi M and Cree, Andrew and Diep Dao, Marvin and De Jong, Pieter J and Cruz-Herrera del Rosario, Ricardo and Delehaunty, Kim D and Dinh, Huyen H and Eichler, Evan E and Fitzgerald, Stephen and Flicek, Paul and Fontenot, Catherine C and Fowler, R. Gerald and Fronick, Catrina and Fulton, Lucinda A and Fulton, Robert S and Gabisi, Ramatu Ayiesha and Gerlach, Daniel and Graves, Tina A and Gunaratne, Preethi H and Hahn, Matthew W and Haig, David and Han, Yi and Harris, R. Alan and Herrero, Javier and Hillier, LaDeana W and Hubley, Robert and Hughes, Jennifer F and Hume, Jennifer and Jhangiani, Shalini N and Jorde, Lynn B and Joshi, Vandita and Karakor, Emre and Konkel, Miriam K and Kosiol, Carolin and LKovar, Christie and Kriventseva, Evgenia V and Lee, Sandra L and Lewis, Lora R and Liu, Yih-Shin and Lopez, John and Lopez-Otin, Carlos and Lorente-Galdos, Belen and Mansfield, Keith G and Marques-Bonet, Tomas and Minx, Patrick and Misceo, Doriana and Moncrieff, J. Scott and Morgan, Margaret B and Nazareth, Lynne V and Newsham, Irene and Nguyen, Ngoc Bich and Okwuonu, Geoffrey O and Prabhakar, Shyam and Perales, Lora and Pu, Ling-Ling and Puente, Xose S and Quesada, Victor and Ranck, Megan C and Raney, Brian J and Raveendran, Muthuswamy and Deiros, David Rio and Rocchi, Mariano and Rodriguez, David and Ross, Corinna and Ruffier, Magali and Ruiz, San Juana and Sajjadian, Saba and Santibanez, Jireh and Schrider, Daniel R and Searle, Steve and Skaletsky, Helen and Soibam, Benjamin and Smit, Arian F.A and Tennakoon, Jayantha B and Tomaska, Lubomir and Ullmer, Brygg and Vejnar, Charles E and Ventura, Mario and Vilella, Albert J and Vinar, Tomas and Vogel, Jan-Hinnerk and Walker, Jerilyn A and Wang, Qing and ... and Marmoset Genome Sequencing Anal Co and Marmoset Genome Sequencing and Analysis Consortium and The Marmoset Genome Sequencing and Analysis Consortium
Nature Genetics, ISSN 1061-4036, 2014, Volume 46, Issue 8, pp. 850 - 857
We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data... 
CHIMERISM | INCREASED OVULATION RATE | MULTILOCUS GENOTYPE DATA | GENE | VARIANTS | GROWTH | GENETICS & HEREDITY | VERTEBRATES | SEGMENTAL DUPLICATIONS | MUTATIONS | CHIMPANZEE | Amino Acid Sequence | Animals | Callithrix - genetics | Molecular Sequence Data | Reproduction - genetics | Female | MicroRNAs - genetics | Polymorphism, Single Nucleotide | Phylogeny | Genome | Sequence Analysis, DNA - methods | Evolution, Molecular | Physiological aspects | Marmosets | Genetic aspects | MicroRNA | Research | Hematopoietic stem cells | Proteins | Growth hormones | Genomes | Monkeys & apes | Evolution & development | Genomics | Polimorfisme genètic | Evolució molecular
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