Gene overlapping and size constraints in the viral world

[1]  张静,et al.  Banana Ovate family protein MaOFP1 and MADS-box protein MuMADS1 antagonistically regulated banana fruit ripening , 2015 .

[2]  R. Taylor,et al.  RNA replication errors and the evolution of virus pathogenicity and virulence. , 2014, Current opinion in virology.

[3]  Riccardo Bernasconi,et al.  How Viruses Hijack the ERAD Tuning Machinery , 2014, Journal of Virology.

[4]  E. Domingo,et al.  Exploration of sequence space as the basis of viral RNA genome segmentation , 2014, Proceedings of the National Academy of Sciences.

[5]  Jie Cui,et al.  An Allometric Relationship between the Genome Length and Virion Volume of Viruses , 2014, Journal of Virology.

[6]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[7]  J. F. Wright,et al.  AAV empty capsids: for better or for worse? , 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

[8]  Angelo Pavesi,et al.  Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses , 2013, PLoS Comput. Biol..

[9]  M. Daugherty,et al.  Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes , 2013, Proceedings of the National Academy of Sciences.

[10]  W. Roos,et al.  Probing the biophysical interplay between a viral genome and its capsid. , 2013, Nature chemistry.

[11]  Hans Bitter,et al.  ViralZone: recent updates to the virus knowledge resource , 2012, Nucleic Acids Res..

[12]  Andreas Wagner,et al.  Evolution of Viral Proteins Originated De Novo by Overprinting , 2012, Molecular biology and evolution.

[13]  D. Raoult,et al.  Reclassification of Giant Viruses Composing a Fourth Domain of Life in the New Order Megavirales , 2012, Intervirology.

[14]  Marco Punta,et al.  AntiFam: a tool to help identify spurious ORFs in protein annotation , 2012, Database J. Biol. Databases Curation.

[15]  Michal Linial,et al.  Viral Proteins Acquired from a Host Converge to Simplified Domain Architectures , 2012, PLoS Comput. Biol..

[16]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..

[17]  D. Rowlands,et al.  Formation of Higher-Order Foot-and-Mouth Disease Virus 3Dpol Complexes Is Dependent on Elongation Activity , 2011, Journal of Virology.

[18]  E. Koonin,et al.  Viruses with More Than 1,000 Genes: Mamavirus, a New Acanthamoeba polyphaga mimivirus Strain, and Reannotation of Mimivirus Genes , 2011, Genome biology and evolution.

[19]  E. Holmes What Does Virus Evolution Tell Us about Virus Origins? , 2011, Journal of Virology.

[20]  Norman E. Davey,et al.  How viruses hijack cell regulation. , 2011, Trends in biochemical sciences.

[21]  M. Lynch Evolution of the mutation rate. , 2010, Trends in genetics : TIG.

[22]  Robert Belshaw,et al.  Why genes overlap in viruses , 2010, Proceedings of the Royal Society B: Biological Sciences.

[23]  Patrick Forterre,et al.  Giant Viruses: Conflicts in Revisiting the Virus Concept , 2010, Intervirology.

[24]  A. Mchardy,et al.  The Role of Genomics in Tracking the Evolution of Influenza A Virus , 2009, PLoS pathogens.

[25]  A. Keith Dunker,et al.  Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation , 2009, Journal of Virology.

[26]  M. Bouvier,et al.  MHC class I antigen presentation: learning from viral evasion strategies , 2009, Nature Reviews Immunology.

[27]  Gavin J. D. Smith,et al.  Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic , 2009, Nature.

[28]  D. Moreira,et al.  Ten reasons to exclude viruses from the tree of life , 2009, Nature Reviews Microbiology.

[29]  Kazuho Ikeo,et al.  Constrained evolution with respect to gene overlap of hepatitis B virus , 2009, Journal of Molecular Evolution.

[30]  C. Viboud,et al.  Explorer The genomic and epidemiological dynamics of human influenza A virus , 2016 .

[31]  Hui Li,et al.  Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection , 2008, Proceedings of the National Academy of Sciences.

[32]  S. Hammer,et al.  The challenge of HIV-1 subtype diversity. , 2008, The New England journal of medicine.

[33]  E. Holmes,et al.  Rates of evolutionary change in viruses: patterns and determinants , 2008, Nature Reviews Genetics.

[34]  R. Lamb,et al.  Mechanisms for enveloped virus budding: can some viruses do without an ESCRT? , 2008, Virology.

[35]  Andrew Rambaut,et al.  Pacing a small cage: mutation and RNA viruses , 2008, Trends in Ecology & Evolution.

[36]  W. Gelbart,et al.  Packaging of a polymer by a viral capsid: the interplay between polymer length and capsid size. , 2008, Biophysical journal.

[37]  Klaus Schulten,et al.  Stability and dynamics of virus capsids described by coarse-grained modeling. , 2006, Structure.

[38]  Edward C Holmes,et al.  Avian influenza virus exhibits rapid evolutionary dynamics. , 2006, Molecular biology and evolution.

[39]  V. Belyĭ,et al.  Electrostatic origin of the genome packing in viruses , 2006, Proceedings of the National Academy of Sciences.

[40]  Cecile Viboud,et al.  Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus , 2006, Biology Direct.

[41]  Patrick Forterre,et al.  The origin of viruses and their possible roles in major evolutionary transitions. , 2006, Virus research.

[42]  Eugene V Koonin,et al.  Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. , 2006, Virus research.

[43]  David Reguera,et al.  Classical nucleation theory of virus capsids. , 2006, Biophysical journal.

[44]  M. Vignuzzi,et al.  Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population , 2006, Nature.

[45]  W. Miller,et al.  Translational control in positive strand RNA plant viruses. , 2006, Virology.

[46]  R. Fujinami,et al.  Molecular Mimicry, Bystander Activation, or Viral Persistence: Infections and Autoimmune Disease , 2006, Clinical Microbiology Reviews.

[47]  Chandrajit L. Bajaj,et al.  VIPERdb: a relational database for structural virology , 2005, Nucleic Acids Res..

[48]  Jean-Michel Claverie,et al.  Mimivirus and the emerging concept of "giant" virus. , 2005, Virus research.

[49]  Chris M. Brown,et al.  Detecting overlapping coding sequences in virus genomes , 2006, BMC Bioinformatics.

[50]  S. Salzberg,et al.  Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution , 2005, Nature.

[51]  Santiago F. Elena,et al.  Adaptive Value of High Mutation Rates of RNA Viruses: Separating Causes from Consequences , 2005, Journal of Virology.

[52]  Michal Galdzicki,et al.  Mammalian overlapping genes: the comparative perspective. , 2004, Genome research.

[53]  J. V. Etten,et al.  Unusual Life Style of Giant Chlorella Viruses , 2003 .

[54]  Eugene V. Koonin,et al.  Comparative genomics, minimal gene-sets and the last universal common ancestor , 2003, Nature Reviews Microbiology.

[55]  David R Nelson,et al.  Virus shapes and buckling transitions in spherical shells. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[56]  J. V. Van Etten,et al.  Unusual life style of giant chlorella viruses. , 2003, Annual review of genetics.

[57]  S. Harvey,et al.  Investigation of viral DNA packaging using molecular mechanics models. , 2002, Biophysical chemistry.

[58]  Eugene V Koonin,et al.  Purifying and directional selection in overlapping prokaryotic genes. , 2002, Trends in genetics : TIG.

[59]  D. Krakauer,et al.  Redundancy, antiredundancy, and the robustness of genomes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[60]  S. Frank Multiplicity of infection and the evolution of hybrid incompatibility in segmented viruses , 2001, Heredity.

[61]  Luigi Naldini,et al.  Viral vectors for gene therapy: the art of turning infectious agents into vehicles of therapeutics , 2001, Nature Medicine.

[62]  David C. Krakauer,et al.  STABILITY AND EVOLUTION OF OVERLAPPING GENES , 2000, Evolution; international journal of organic evolution.

[63]  E. Holmes,et al.  Evolutionary aspects of recombination in RNA viruses. , 1999, The Journal of general virology.

[64]  H. Ploegh Viral strategies of immune evasion. , 1998, Science.

[65]  A. Pavesi,et al.  On the Informational Content of Overlapping Genes in Prokaryotic and Eukaryotic Viruses , 1997, Journal of Molecular Evolution.

[66]  E. Domingo,et al.  Rapid evolution of viral RNA genomes. , 1997, The Journal of nutrition.

[67]  J. Kappes,et al.  The Vif protein of human and simian immunodeficiency viruses is packaged into virions and associates with viral core structures , 1995, Journal of virology.

[68]  R. Lamb,et al.  The remarkable coding strategy of borna disease virus: a new member of the nonsegmented negative strand RNA viruses. , 1995, Virology.

[69]  P. Keese,et al.  Origins of genes: "big bang" or continuous creation? , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[70]  Katherine Spindler,et al.  Rapid evolution of RNA genomes. , 1982, Science.

[71]  C. A. Hutchison,et al.  Overlapping genes in bacteriophage φX174 , 1976, Nature.

[72]  B. Barrell,et al.  Overlapping genes in bacteriophage phiX174. , 1976, Nature.

[73]  D. Baltimore Expression of animal virus genomes. , 1971, Bacteriological reviews.

[74]  A. Klug,et al.  Physical principles in the construction of regular viruses. , 1962, Cold Spring Harbor symposia on quantitative biology.