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Size of the Whole versus Number of Parts in Genomes

Antoni Hernández-Fernández, Jaume Baixeries, Núria Forns, Ramon Ferrer-i-Cancho
2011 Entropy  
of the whole) in genomes are seriously flawed.  ...  Here the relationship between number of parts (the chromosomes) and size of the whole (the genome) is studied for other groups of organisms from different kingdoms. Two major results are obtained.  ...  This work was supported by the project SESAAME-BAR (TIN2008-06582-C03-01) of the Spanish Ministry of Science and Innovation.  ... 
doi:10.3390/e13081465 fatcat:xrlwzrmffrazxglfwmrwl54fny

Single-Molecule Approach to Bacterial Genomic Comparisons via Optical Mapping

S. Zhou, A. Kile, M. Bechner, M. Place, E. Kvikstad, W. Deng, J. Wei, J. Severin, R. Runnheim, C. Churas, D. Forrest, E. T. Dimalanta (+4 others)
2004 Journal of Bacteriology  
Modern comparative genomics has been established, in part, by the sequencing and annotation of a broad range of microbial species.  ...  Given the availability of a large number of microbial species, new whole genome approaches must be developed to fully leverage this information at the level of strain diversity that maximize discovery.  ...  ACKNOWLEDGMENTS This study was supported by a grant from the DOE DE-FC02-01ER63175 to D.C.S.  ... 
doi:10.1128/jb.186.22.7773-7782.2004 pmid:15516592 pmcid:PMC524920 fatcat:y6qx5kezgbfqre3tio3h4olvba

Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data

Nicolas Berthet, Stéphane Descorps-Declère, Andriniaina Andy Nkili-Meyong, Emmanuel Nakouné, Antoine Gessain, Jean-Claude Manuguerra, Mirdad Kazanji
2016 Biological Research  
The pre-process method proposed in this study strongly limits the negative impact of chimeric reads in order to obtain the full-length of viral genomes.  ...  Although in all cases, our pre-processed method improved genome assembly, only its combination with the use of SPAdes allowed us to obtain the full-length of the viral genomes tested in one contig.  ...  The funders had no role in study design, data analysis or preparation of the manuscript.  ... 
doi:10.1186/s40659-016-0099-y pmid:27605096 pmcid:PMC5015205 fatcat:pdddtlf4tnbyria2r2f6jrlft4

Atypical face shape and genomic structural variants in epilepsy

Krishna Chinthapalli, Emanuele Bartolini, Jan Novy, Michael Suttie, Carla Marini, Melania Falchi, Zoe Fox, Lisa M. S. Clayton, Josemir W. Sander, Renzo Guerrini, Chantal Depondt, Raoul Hennekam (+2 others)
2012 Brain  
This is true when analysing the whole face, or the periorbital region or the perinasal region alone. We then tested the predictive accuracy of our measure in a second group of 63 patients.  ...  Many pathogenic structural variants of the human genome are known to cause facial dysmorphism.  ...  Acknowledgements The authors thank patients and their families for participating in this study, control subjects and the physicians that assisted with recruitment.  ... 
doi:10.1093/brain/aws232 pmid:22975390 pmcid:PMC3470710 fatcat:zxx3445fl5fbtnkgxwul6lf6ga

Haplotype complementarity under mutational pressure

Stanislaw Cebrat
2011 Frontiers in bioscience (Scholar edition)  
Role of mutational pressure on the emerging of complementarity 3.4. The role of inbreeding 4. Consequences 4.1. Sympatric speciation 4.2. Distribution of recombination events 4.3.  ...  Definition: purification versus complementation 2.2. Mutations 3. Some computer models 3.1. Emerging complementarity 3.2. Gamete recognition 3.3.  ...  Solid circles mark the positions of human chromosomes in that virtual space (number of genes per centiMorgan versus total number of genes in chromosome).  ... 
doi:10.2741/s160 pmid:21196385 fatcat:gqkgljnjorfg3mf3rs3rhkdqpe

Evolutionary Analysis by Whole-Genome Comparisons

A. K. Bansal, T. E. Meyer
2002 Journal of Bacteriology  
terms of gene content, it is first necessary to correct for the size of the genome; (iv) eukaryotes have a significantly smaller percentage of bacterial orthologs after correction for genome size, which  ...  Several conclusions result: (i) a greater absolute number of orthologs of a given species is found in larger species than in smaller ones; (ii) a greater percentage of the orthologous genes of smaller  ...  ACKNOWLEDGMENT This work was supported in part by grant GM-21277 from the National Institutes of Health.  ... 
doi:10.1128/jb.184.8.2260-2272.2002 pmid:11914358 pmcid:PMC134949 fatcat:wcpojwtf7zc27jmdzbp5zpsaj4

Impact of whole genome amplification on analysis of copy number variants

T. J. Pugh, A. D. Delaney, N. Farnoud, S. Flibotte, M. Griffith, H. I. Li, H. Qian, P. Farinha, R. D. Gascoyne, M. A. Marra
2008 Nucleic Acids Research  
To facilitate analyses of such samples, whole genome amplification (WGA) techniques were developed.  ...  Large-scale copy number variants (CNVs) have recently been recognized to play a role in human genome variation and disease.  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge the expert technical assistance of Susanna Chan, Jennifer Asano and Adrian Aly of the Affymetrix Array group at the Genome Sciences Centre, BC Cancer  ... 
doi:10.1093/nar/gkn378 pmid:18559357 pmcid:PMC2490749 fatcat:nge57r6ij5emtdrjjwrzy7fm6y

An alternative approach to multiple genome comparison

Alban Mancheron, Raluca Uricaru, Eric Rivals
2011 Nucleic Acids Research  
However, efficiency, flexibility and objectives of current methods do not suit the whole spectrum of applications, genome sizes and organizations. Innovative approaches are still needed.  ...  We also find out that a substantial number of genes thought to be strain specific have potential orthologs in the other strains.  ...  In bacteriology, the genomic part shared among all strains, the 'core' genome, represents the essential genic component, while the specific part, or 'dispensable' genome, abound in genes associated with  ... 
doi:10.1093/nar/gkr177 pmid:21646341 pmcid:PMC3159434 fatcat:lpygo7clkbbyxgkutlkpo2u77y

Targeting Ascomycota genomes: what and how big?

Rowena Hill, Ilia J. Leitch, Ester Gaya
2021 Fungal Biology Reviews  
In doing so, we additionally looked at the existing genome size data for ascomycetes, given the importance of knowing the size of the genome to ensure sufficient sequencing coverage and assess the completeness  ...  Gap analysis Genome size Whole genome sequencing Abbreviations: whole genome sequencing WGS a b s t r a c t Gap analysis of the available genomic data (i.e. identifying taxonomic groups with no representative  ...  In contrast, boxplots for 6,600 genome sizes (from 3,273 strains) based on genome assemblies are given in translucent colours; here the number of samples per order are the same as the number in brackets  ... 
doi:10.1016/j.fbr.2021.03.003 fatcat:al76r76v45eqfmuc3ema7uppl4

Classification of genomic islands using decision trees and their ensemble algorithms

Dongsheng Che, Cory Hockenbury, Robert Marmelstein, Khaled Rasheed
2010 BMC Genomics  
Genomic islands (GIs) are clusters of alien genes in some bacterial genomes, but not be seen in the genomes of other strains within the same genus.  ...  Despite the discovery of the GI associated features, accurate detection of GIs is still far from satisfactory.  ...  The classifiers can then be used as the basis for classifying any genomic segment in a whole genome.  ... 
doi:10.1186/1471-2164-11-s2-s1 pmid:21047376 pmcid:PMC2975412 fatcat:ppwcuhl4fzgurdvtunaue6qyzq

Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment

Jordan G Okie, Amisha T Poret-Peterson, Zarraz MP Lee, Alexander Richter, Luis D Alcaraz, Luis E Eguiarte, Janet L Siefert, Valeria Souza, Chris L Dupont, James J Elser
2020 eLife  
Mean bacterial genome size, GC content, total number of tRNA genes, total number of rRNA genes, and codon usage bias in ribosomal protein sequences were higher in the fertilized treatment, as predicted  ...  We analyzed their role in mediating planktonic microbial community responses to nutrient enrichment in an oligotrophic, phosphorus-deficient pond in Cuatro Ciénegas, Mexico—one of the first whole-ecosystem  ...  in mean genome size (Fig. 1) .  ... 
doi:10.7554/elife.49816 pmid:31989922 pmcid:PMC7028357 fatcat:jdfiu7igivbi5gfl5zou4mavza

INBREEDING AND OUTBREEDING DEPRESSIONS IN THE PENNA MODEL AS A RESULT OF CROSSOVER FREQUENCY

K. BOŃKOWSKA, M. KULA, S. CEBRAT, D. STAUFFER
2007 International Journal of Modern Physics C  
We study the changes in the population size due to this mixing and interpret them through a counterplay of purifying selection and of haplotype complementarity.  ...  The population in the sexual Penna ageing model is first separated into several reproductively isolated groups. Then, after equilibration, sexual mixing between the groups is allowed.  ...  For more efficient reproduction, the number of different haplotypes should be restricted and in fact there are only two different complementing haplotypes in the whole population as it was shown in Ref  ... 
doi:10.1142/s0129183107011352 fatcat:7uvci73s5rgk7g7vj4dvpyjyoq

The Parameters of the Menzerath-Altmann Law in Genomes

Jaume Baixeries, Antoni Hernández-Fernández, Núria Forns, Ramon Ferrer-i-Cancho
2013 Journal of Quantitative Linguistics  
The relationship between the size of the whole and the size of the parts in language and music is known to follow Menzerath-Altmann law at many levels of description (morphemes, words, sentences...).  ...  Qualitatively, the law states that larger the whole, the smaller its parts, e.g., the longer a word (in syllables) the shorter its syllables (in letters or phonemes).  ...  This work was supported by the grant Iniciació i reincorporació a la recerca from the Universitat Politècnica de Catalunya and the grant BASMATI (TIN2011-27479-C04-03) from the Spanish Ministry of Science  ... 
doi:10.1080/09296174.2013.773141 fatcat:75dr4ylmkfdfno6ksv2f5dzysu

GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes

Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purkayastha, Raja Mazumder, Charles Buck, Donald Seto
2004 BMC Bioinformatics  
In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing.  ...  An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases.  ...  This work has been supported in part by a grant from ATCC and a Faculty  ... 
doi:10.1186/1471-2105-5-52 pmid:15128433 pmcid:PMC419981 fatcat:rokv35xw4fb7ti445k6giepfom

Clonal Evolutionary Analysis during HER2 Blockade in HER2-Positive Inflammatory Breast Cancer: A Phase II Open-Label Clinical Trial of Afatinib +/- Vinorelbine

Gerald Goh, Ramona Schmid, Kelly Guiver, Wichit Arpornwirat, Imjai Chitapanarux, Vinod Ganju, Seock-Ah Im, Sung-Bae Kim, Arunee Dechaphunkul, Jedzada Maneechavakajorn, Neil Spector, Thomas Yau (+8 others)
2016 PLoS Medicine  
We performed an open-label, single-arm phase II clinical trial (ClinicalTrials.gov NCT01325428) to investigate the efficacy and safety of afatinib, an irreversible ErbB family inhibitor, alone and in combination  ...  The primary endpoint was clinical benefit; secondary endpoints were objective response (OR), duration of OR, and progression-free survival (PFS).  ...  Medical writing assistance, supported financially by Boehringer Ingelheim, was provided by Caroline Allinson of GeoMed, an Ashfield Company, part of UDG Healthcare Plc, during the preparation of this manuscript  ... 
doi:10.1371/journal.pmed.1002136 pmid:27923043 pmcid:PMC5140058 fatcat:uwohtzzurvh55psetzgkhmw434
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