Results 81 to 90 of about 157,766 (271)

A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer

, 2005
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
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   +43 more
core   +2 more sources

Revealing mammalian evolutionary relationships by comparative analysis of gene clusters [PDF]

, 2012
Many software tools for comparative analysis of genomic sequence data have been released in recent decades. Despite this, it remains challenging to determine evolutionary relationships in gene clusters due to their complex histories involving ...
Abi-Rached, Akahoshi, Bailey, Benjamin Dickins, Birney, Cadavid, Cathy Riemer, Chen, Chih-Hao Hsu, Chiu, Colobran, Datta, Degenhardt, Dewey, Dufayard, Edwards, Eric D. Green, Fitch, Fitch, Fitch, Giltae Song, Gish, Gonzalez, Goodstadt, Graef, Guethlein, Guethlein, Han, Hardies, Hardison, Hardison, Hardison, Harris, Hie Lim Kim, Hoffmann, Hou, Hou, Hsu, Hsu, Hu, Huerta-Cepas, Jensen, Johnson, Kim, Kristensen, Lee, Levy, Li, Li, Lopez-Vazquez, Louxin Zhang, Margulies, Martin, Matsuya, Mi, Miyata, Muller, Murphy, NISC Comparative Sequencing Program, , Opazo, Opazo, Ostlund, Ouzounis, Parham, Pianezza, Rajalingam, Ross C. Hardison, Sambrook, Shilling, Siepel, Smit, Song, Song, Song, Sonnhammer, Su, Tatusov, The ENCODE Project Consortium, Uchiyama, van der Heijden, Vilella, Wang, Wapinski, Waterhouse, Webb Miller, Wilson, Wilson, Woelk, Yu Zhang, Zhang   +89 more
core   +2 more sources

Tumor and germline testing with next generation sequencing in epithelial ovarian cancer: a prospective paired comparison using an 18‐gene panel

Molecular Oncology, EarlyView.
Genetic testing in epithelial ovarian cancer includes both germline and tumor‐testing. This approach often duplicates resources. The current prospective study assessed the feasibility of tumor‐first multigene testing by comparing tumor tissue with germline testing of peripheral blood using an 18‐gene NGS panel in 106 patients.
Elisabeth Spenard, Cristina Mitric, Melanie Care, Tracy L. Stockley, Raymond H. Kim, Jeanna McCuaig, Blaise Clarke, Laura Ranich, Clare Sheen, Sarah E. Ferguson, Liat Hogen, Taymaa May, Marcus Q. Bernardini   +12 more
wiley   +1 more source

Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba.

PLoS Genetics, 2017
One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes.
Rebekah L Rogers, Ling Shao, Kevin R Thornton   +2 more
doaj   +1 more source

A recent duplication revisited: phylogenetic analysis reveals an ancestral duplication highly-conserved throughout the Oryza genus and beyond

BMC Plant Biology, 2009
Background The role of gene duplication in the structural and functional evolution of genomes has been well documented. Analysis of complete rice (Oryza sativa) genome sequences suggested an ancient whole genome duplication, common to all the grasses ...
Cooke Richard, Laudié Michèle, Jacquemin Julie   +2 more
doaj   +1 more source

Clusters of microRNAs emerge by new hairpins in existing transcripts [PDF]

, 2013
Genetic linkage may result in the expression of multiple products from a polycistronic transcript, under the control of a single promoter. In animals, protein-coding polycistronic transcripts are rare.
Alberts, Altschul, Altuvia, Antonio Marco, Aravin, Auyeung, Axtell, Bartel, Bartel, Barton, Baskerville, Blumenthal, Blumenthal, Boutla, Campo-Paysaa, Charlesworth, Cutter, Felsenstein, Griffiths-Jones, Griffiths-Jones, Grimson, Han, Hertel, Hill, Katoh, Kim, Kloosterman, Kozomara, Krol, Lagos-Quintana, Larkin, Lau, Lawrence, Leaman, Lee, Lee, Li, Lynch, Lynch, Maher, Marco, Marco, Marco, Marco, Marco, Maria Ninova, Matthew Ronshaugen, Maynard Smith, Nozawa, Nozawa, Qian, Roux, Ruby, Ryazansky, Saini, Saini, Saitou, Salgado, Sam Griffiths-Jones, Satou, Savard, Sempere, Tamura, Tanzer, Wheeler, Wheeler, Zeng   +66 more
core   +2 more sources

Liquid biopsy epigenetics: establishing a molecular profile based on cell‐free DNA

Molecular Oncology, EarlyView.
Cell‐free DNA (cfDNA) fragments in plasma from cancer patients carry epigenetic signatures reflecting their cells of origin. These epigenetic features include DNA methylation, nucleosome modifications, and variations in fragmentation. This review describes the biological properties of each feature and explores optimal strategies for harnessing cfDNA ...
Christoffer Trier Maansson, Anders Lade Nielsen, Boe Sandahl Sorensen   +2 more
wiley   +1 more source

Erratum: Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs [PDF]

Heredity, 2015
Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of ...
N J Kenny, K W Chan, W Nong, Z Qu, I Maeso, H Y Yip, T F Chan, H S Kwan, P W H Holland, K H Chu, J H L Hui   +10 more
openaire   +5 more sources

The Phenotype Paradox: Lessons From Natural Transcriptome Evolution on How to Engineer Plants

Frontiers in Plant Science, 2020
Plants have evolved genome complexity through iterative rounds of single gene and whole genome duplication. This has led to substantial expansion in transcription factor numbers following preferential retention and subsequent functional divergence of ...
Justin Law, Kangbo Ng, Kangbo Ng, Oliver P. F. Windram   +3 more
doaj   +1 more source

Cis‐regulatory and long noncoding RNA alterations in breast cancer – current insights, biomarker utility, and the critical need for functional validation

Molecular Oncology, EarlyView.
The noncoding region of the genome plays a key role in regulating gene expression, and mutations within these regions are capable of altering it. Researchers have identified multiple functional noncoding mutations associated with increased cancer risk in the genome of breast cancer patients.
Arnau Cuy Saqués, Aracele Martinez‐Mendez, John Crown, Alex Eustace   +3 more
wiley   +1 more source