3 research outputs found
A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer
- Author
- A.B. Simonson
- B. Boussau
- B. Snel
- B. Snel
- B.E. Dutilh
- B.G. Mirkin
- C. Pál
- C.G. Kurland
- D.H. Huson
- E. Belda
- E.A. Herniou
- E.D. Green
- E.J. Deeds
- E.L.L. Sonnhammer
- E.V. Koonin
- F. Delsuc
- F. Tekaia
- G.D.P. Clarke
- G.P. Karev
- G.P. Karev
- G.P. Karev
- I.K. Jordan
- J. Lin
- J.A. Lake
- J.O. Korbel
- J.P. Gogarten
- J.T. Herbeck
- K.H. Wolfe
- M. Csűrös
- M. Pellegrini
- M.G. Montague
- M.W. Hahn
- R.L. Tatusov
- S. Karlin
- S. Yang
- S.T. Fitz-Gibbon
- T. Pupko
- V. Kunin
- V. Kunin
- W. Feller
- W.J. Reed
- X. Gu
- Y. Boucher
- Y.I. Wolf
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 27/09/2005
- Field of study
We introduce a Markov model for the evolution of a gene family along a
phylogeny. The model includes parameters for the rates of horizontal gene
transfer, gene duplication, and gene loss, in addition to branch lengths in the
phylogeny. The likelihood for the changes in the size of a gene family across
different organisms can be calculated in O(N+hM^2) time and O(N+M^2) space,
where N is the number of organisms, h is the height of the phylogeny, and M
is the sum of family sizes. We apply the model to the evolution of gene content
in Preoteobacteria using the gene families in the COG (Clusters of Orthologous
Groups) database
Phylogeny vs genome reshuffling: horizontal gene transfer
- Author
- A. Aertsen
- A. Campbell
- A. Tsirigos
- A.B. Blanc-Potard
- A.L. Hughes
- A.M. Viale
- A.O. Richardson
- B. Linz
- B. Pruss
- B. Snel
- B.G. Spratt
- B.P. Rosen
- C. Dogra
- C. Dutta
- C. Hall
- C. Medigue
- C.C. Davis
- C.G. Dowson
- C.G. Kurland
- C.H. House
- C.J. Bult
- C.P. Ponting
- C.R. Jackson
- C.R. Woese
- C.R. Woese
- C.R. Woese
- C.R. Woese
- C.Y. He
- D. Dubnau
- D. Gioia Di
- D. Mazel
- D. Schlieper
- D.A. Natale
- E. Bapteste
- E. Lerat
- E.A. Groisman
- E.A. Groisman
- E.A. Groisman
- E.A. Groisman
- E.A. Stohl
- E.F. Mongodin
- E.V. Koonin
- E.V. Koonin
- E.V. Sheveleva
- F. Cruz De la
- F. Tekaia
- F.S. Brinkman
- F.S. Lawson
- G. Blum
- G. PĂĽhler
- G. Ricard
- G.D.P. Clarke
- G.E. Fox
- G.J. Olsen
- G.V. Glazko
- H. Ochman
- H. Ochman
- H. Philippe
- H. Won
- H.-H. Fuxelius
- H.-P. Klenk
- H.-P. Klenk
- I. Yanai
- I.-G. Choi
- J. Ellis
- J. Hacker
- J. Lin
- J. Lin
- J. Macalady
- J. Mrazek
- J. Nolling
- J. Xiong
- J.A. Eisen
- J.A. Eisen
- J.E. Moss
- J.G. Lawrence
- J.G. Lawrence
- J.G. Lawrence
- J.G. Lawrence
- J.G. Lawrence
- J.G. Lawrence
- J.O. Korbel
- J.P. Gomes
- J.R. Brown
- J.R. Meer Van der
- J.T. Beck
- J.W. Brown
- K. Matsui
- K.E. Nelson
- K.J. Kechris
- K.S. Makarova
- L. Aravind
- L.D. Bowler
- L.G. Rahme
- L.M. Iyer
- M. Eppinger
- M. Klein
- M. MĂĽller
- M. Pellegrini
- M. Syvanen
- M. Woloszynska
- M.A. Huynen
- M.A. Ragan
- M.C. Rivera
- M.C. Rivera
- M.J. Danson
- M.J. Danson
- M.S. Shanley
- M.V. Omelchenko
- M.W. Smith
- N. Kondo
- N. Raizada
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- O. Pisurek
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- O.T. Avery
- P. Baumann
- P. Lopez-Garc
- P. Schönheit
- P. Sharma
- P. Wenzl
- P.A. Williams
- P.D. Schloss
- P.J. Kennelly
- P.M. Sharp
- R. Grantham
- R. Jain
- R. Lan
- R. Lujan
- R. Venkatesh
- R.C. Wyndham
- R.F. Doolittle
- R.G. Beiko
- R.L. Charlebois
- R.L. Tatusov
- R.L. Tatusov
- R.M. Hall
- R.S. Gupta
- S. Backert
- S. Garcia-Vallve
- S. Karlin
- S. Karlin
- S. Porwal
- S.A. Vokes
- S.J. Oh
- S.T. Fitz-Gibbon
- Sadhana Lal
- Simrita Cheema
- T. Dagan
- T.K. McDaniel
- T.M. Gihring
- U. Gophna
- U. Gophna
- V. Kunin
- V. Sonakya
- V.C. Kalia
- V.C. Kalia
- V.C. Kalia
- V.C. Kalia
- V.C. Kalia
- V.C. Kalia
- V.C. Kalia
- V.C. Kalia
- Vipin C. Kalia
- W. Martin
- W. Martin
- W. Zhang
- W.F. Doolittle
- W.F. Doolittle
- W.H. Yap
- X. Qiu
- X. Wang
- Y. Shen
- Y.I. Wolf
- Y.I. Wolf
- Y.I. Wolf
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
The Emergence of Life
- Author
- A. Biscans
- A. de la Escosura
- A. Eschenmoser
- A. Eschenmoser
- A. Eschenmoser
- A. Hofmann
- A. Lazcano
- A. Lazcano
- A. Nissenbaum
- A. Oparin
- A. Pyle
- A. Sievers
- A. Spang
- A. Spang
- A. Spang
- A. Szent-Györgyi
- A. Szilagyi
- A. Udry
- A. Whicher
- A.A. DavĂn
- A.C. Fahrenbach
- A.D. Fortes
- A.G. Cairns-Smith
- A.G. Patterson
- A.I.S. Kemp
- A.J. Cavosie
- A.J. Probst
- A.K. Van Groos
- A.L. Ducluzeau
- A.L. Weber
- A.M. Anger
- A.M. Makarieva
- A.M. Poole
- A.M. Turner
- A.R. Mushegian
- A.S. Petrov
- A.S. Petrov
- A.S. Petrov
- A.S. Petrov
- A.S. Petrov
- A.T. Johnson
- A.V. Dass
- A.V. Dass
- B. Boussau
- B. Damer
- B. Marty
- B. Marty
- B. Obermayer
- B. Sherwood Lollar
- B. Snel
- B.B. Jensen
- B.F. Damer
- B.J. Cafferty
- B.L. Ligon
- B.M. Uz
- B.S. Kamber
- B.S. Schuwirth
- C. Bounama
- C. Brassé
- C. Briones
- C. Chyba
- C. Francklyn
- C. H. House
- C. He
- C. Hsiao
- C. Hsiao
- C. Hsiao
- C. Mathis
- C. Menor-Salvan
- C. O’Neill
- C.E. Cleland
- C.E. Folsome
- C.E.J. de Ronde
- C.G. Kurland
- C.H. House
- C.J. Castelle
- C.J. Castelle
- C.M. Fisher
- C.M. Runnels
- C.M. Spahn
- C.P. McKay
- C.P. McKay
- C.R. Bernier
- C.R. Glein
- C.R. Woese
- C.R. Woese
- C.R. Woese
- C.R. Woese
- C.R. Woese
- C.R. Woese
- C.R. Woese
- C.R. Woese
- C.R. Woese
- C.S. Cockell
- C.T. Brown
- C.V. Mungi
- C.W. Carter Jr.
- C.W. Carter Jr.
- Cv. Linné
- Cv. Linné
- D. Cordier
- D. Deamer
- D. Deamer
- D. Deamer
- D. Gourier
- D. Milshteyn
- D. Milshteyn
- D. Parkos
- D. Puthenvedu
- D. Rickard
- D. Trail
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- D. Whitaker
- D.D. Leipe
- D.E. Draper
- D.E.B. Pugel
- D.H. Lee
- D.J. Frost
- D.M.J. Lilley
- D.N. Beratan
- D.P. O’Brien
- D.S. Kelley
- D.W. Schwartzman
- E. Anders
- E. Branscomb
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- E. Camprubi
- E. CamprubĂ
- E. Lellouch
- E. Schrödinger
- E. Zuckerkandl
- E.B. Watson
- E.D. Dorn
- E.F. van Dishoeck
- E.G.H. Wagner
- E.L. Shock
- E.L. Shock
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- E.P. Reeves
- E.T. Wolf
- E.V. Koonin
- F. Raulin
- F. Raulin
- F. Raulin
- F. Raulin
- F. Robert
- F. Schlunzen
- F. Tian
- F. Tian
- F. Werner
- F. Westall
- F. Westall
- F. Westall
- F.H. Westheimer
- F.L. Sousa
- F.S. Jordan
- F.S. Jordan
- G. Cooper
- G. Costanzo
- G. Fuchs
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- S. Orla-Jensen
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- S.L. Miller
- S.S. Abby
- S.S. Athavale
- S.T. Fitz Gibbon
- T. Cavalier-Smith
- T. Dagan
- T. Dutta
- T. Nunoura
- T. Ray
- T.A. Williams
- T.A. Williams
- T.A. Williams
- T.D. Ames
- T.F. Smith
- T.M. Harrison
- T.M. McCollom
- T.R. Cech
- T.R. Cech
- T.R. Cech
- T.R. Cech
- T.R. Cech
- T.Y. Tsong
- T.Z. Jia
- U. Nagaswamy
- U.S. Clanton
- V. Ramakrishnan
- V. Sautter
- V. Sojo
- V.K. Misra
- V.M. Goldschmidt
- V.N. Sagi
- V.N. Zharkov
- W. Filipowicz
- W. Gilbert
- W. Huang
- W. Ma
- W. Ma
- W. Nijman
- W. Nijman
- W. Nitschke
- W.B. Moore
- W.D. Fuller
- W.D. Fuller
- W.F. Bottke
- W.F. Doolittle
- W.F. Martin
- W.F. Martin
- W.F. Martin
- W.F. Martin
- W.G. Meinschein
- W.R. Taylor
- W.T. Liu
- X. Li
- Y. Dandonneau
- Y. Ding
- Y. Koga
- Y.I. Wolf
- Y.L. Yung
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study