Special Issue "Feature Paper 2012"
A special issue of Genes (ISSN 2073-4425).
Deadline for manuscript submissions: closed (30 September 2012)
Prof. Dr. J. Peter W. Young
Department of Biology, University of York, Heslington, York YO10 5DD, UK
Phone: +44 1904 328630
Fax: +44 1904 328505
Interests: bacterial genomes; population genetics; phylogenomics; phylogenetics; genome projects; genetic diversity
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed Open Access quarterly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.
Genes 2012, 3(2), 320-343; doi:10.3390/genes3020320
Received: 30 April 2012; in revised form: 11 May 2012 / Accepted: 17 May 2012 / Published: 29 May 2012| Download PDF Full-text (255 KB) | Download XML Full-text
Communication: Genome-Wide Sequencing Reveals Two Major Sub-Lineages in the Genetically Monomorphic Pathogen Xanthomonas Campestris Pathovar Musacearum
Genes 2012, 3(3), 361-377; doi:10.3390/genes3030361
Received: 10 June 2012; in revised form: 24 June 2012 / Accepted: 26 June 2012 / Published: 4 July 2012| Download PDF Full-text (691 KB) | Download XML Full-text |
Genes 2012, 3(3), 378-390; doi:10.3390/genes3030378
Received: 5 May 2012; in revised form: 4 June 2012 / Accepted: 15 June 2012 / Published: 5 July 2012| Download PDF Full-text (3062 KB) | Download XML Full-text |
Genes 2012, 3(3), 423-443; doi:10.3390/genes3030423
Received: 8 June 2012; in revised form: 23 June 2012 / Accepted: 29 June 2012 / Published: 18 July 2012| Download PDF Full-text (550 KB) | Download XML Full-text |
Genes 2012, 3(3), 521-544; doi:10.3390/genes3030521
Received: 20 June 2012; in revised form: 9 August 2012 / Accepted: 13 August 2012 / Published: 27 August 2012| Download PDF Full-text (292 KB) | Download XML Full-text
Article: Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
Genes 2012, 3(3), 545-575; doi:10.3390/genes3030545
Received: 6 July 2012; in revised form: 15 August 2012 / Accepted: 15 August 2012 / Published: 30 August 2012| Download PDF Full-text (2373 KB) | Download XML Full-text |
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Type of Paper: Review
Title: Origins of Entirely New Genes
Author: Kenji Ikehara
Affiliation: Nara Study Center of The Open University of Japan; E-Mail: firstname.lastname@example.org
Abstract: Two main theories have been proposed for the origins of new genes. One is the duplication theory proposed by S. Ohno (1970) and the other is the exon shuffling theory provided by Gilbert et al. (1997). But, it must be pointed out that both theories are insufficient for explaining the origins of new genes, since the ideas require pre-existing ancestor genes. On the other hand, I have proposed another hypothesis for creation of entirely new genes or the first family genes, suggesting that they were created from non-stop frames on anti-sense sequences of GC-rich genes or GC-NSF(a), and of double-stranded GC-rich (SNS)n and (GNC)n genes in the respective eras of the universal, SNS and GNC genetic codes, where S and N mean G or C and one of four nucleotides, respectively. In parallel, I have presented protein 0th-order structures or specific amino acid compositions, in which random joining of amino acids could produce water-soluble globular proteins at a high probability, such as 10 amino acids encoded by SNS and GNC-encoding [GADV]-amino acids, where [GADV] means glycine [G], alanine [A], aspartic acid [D] and valine [V]. In this review, I will discuss on the principle and the reason why entirely new genes could be produced from those anti-sense sequences of the GC-rich genes, base on a view point of the protein 0th-order structures, which contribute to form globular proteins with slightly flexible structures more than extant proteins.
Type of Paper: Article
Title: Ancestral Prokaryotic Genome Reconstruction at the Gene and Replicon Scales
Authors: Kuan Yang, Lenwood S. Heath, and Joao C. Setubal
Affiliation: Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748 sala 911, 05508-000 São Paulo, SP, Brazil; E-Mail: email@example.com
Abstract: While a large number of computational methods exist for gene-centric phylogenyanalysis, not much has been done for detailed ancestral genome reconstruction. Accurate ancestral genome reconstruction can be understood as a phylogenetic study with more de-tails than a phylogenetic tree reconstruction. We developed a new computational system (REGEN) for ancestral bacterial genome reconstruction at both gene and replicon level. RE-GEN reconstructs gene content, a set of contiguous gene runs, and replicon structure for each genome. Furthermore, along each branch of the phylogenetic tree, it reconstructs possible evolutionary events, including gene level events such as insertion and deletion, and replicon level events such as replicon ﬁssion and fusion. The reconstruction can be carried out using either the maximum parsimony or maximum likelihood method. The system has been extensively evaluated using both real and simulated data and applied to a group of species in the Rhizobiales order in α-proteobacteria. To the authors knowledge, this system is the ﬁrst attempt to perform model-free neighboring gene pairs based ancestral genome reconstruction supporting both maximum parsimony and maximum likelihood methods at both gene and replicon scales.
Type of Paper: Review
Title: Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
Authors: Federica Torri 1,2, Ivo D. Dinov 2,3, Alen Zamanyan 3, Sam Hobel 3, Alex Genco 3, Petros Petrosyan 3, Andrew P. Clark 4, Zhizhong Liu 3, Paul Eggert 3,5, Jonathan Pierce 3, James A. Knowles 4, Joseph Ames 2, Carl Kesselman 2, Arthur W. Toga 2,3, Steven G. Potkin 1,2, Marquis P. Vawter 6 and Fabio Macciardi 1,2 *
Affiliations: 1 Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA 92617, USA; E-Mails: firstname.lastname@example.org (F.T.); email@example.com (S.G.P.); firstname.lastname@example.org (F.M.)
2 Biomedical Informatics Research Network (BIRN), Information Sciences Institute, University of Southern California, Los Angeles, CA 90292, USA; E-Mails: email@example.com (I.D.D.); firstname.lastname@example.org (J.A.); email@example.com (A.W.T.)
3 Laboratory of Neuro Imaging (LONI), University of California, Los Angeles, Los Angeles, CA 90095, USA; E-Mails: Alen.Zamanyan@loni.ucla.edu (A.Z.); firstname.lastname@example.org (S.H.); email@example.com (A.G.); Petros.Petrosyan@loni.ucla.edu (P.P.); firstname.lastname@example.org (Z.L.); email@example.com (P.E.); firstname.lastname@example.org (J.P.);
4 Zilkha Neurogenetic Institute, USC Keck School of Medicine, Los Angeles, CA 90033, USA; E-Mail: email@example.com (C.K.)
5 Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA; E-Mails: firstname.lastname@example.org (A.P.C.); email@example.com (J.K.)
6 Functional Genomics Laboratory, Department of Psychiatry And Human Behavior, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA; E-Mail: firstname.lastname@example.org (M.P.V.)
Abstract: Whole-genome and exome sequencing have already proven to be essential and powerful methods to identify genes responsible for simple Mendelian inherited disorders. These methods can be applied to complex disorders as well, and have been adopted as one of the current mainstream approaches in population genetics. These achievements have been made possible by next generation sequencing (NGS) technologies, which require substantial bioinformatics resources to analyze the dense and complex sequence data. The huge analytical burden of data from genome sequencing might be seen as a bottleneck slowing the publication of NGS papers at this time, especially in psychiatric genetics. We review the existing methods for processing NGS data, to place into context the rationale for the design of a computational resource. We describe our method, the Graphical Pipeline for Computational Genomics (GPCG), to perform the computational steps required to analyze NGS data. The GPCG implements flexible workflows for basic sequence alignment, sequence data quality control, single nucleotide polymorphism analysis, copy number variant identification, annotation, and visualization of results. These workflows cover all the analytical steps required for NGS data, from processing the raw reads to variant calling and annotation. The current version of the pipeline is freely available at http://pipeline.loni.ucla.edu. These applications of NGS analysis may gain clinical utility in the near future (e.g., identifying miRNA signatures in diseases) when the bioinformatics approach is made feasible. Taken together, the annotation tools and strategies that have been developed to retrieve information and test hypotheses about the functional role of variants present in the human genome will help to pinpoint the genetic risk factors for psychiatric disorders.
Type of Paper: Review
Title: The Information Content of Genomes
Author: Mark E. Samuels
Affiliation: Department of Medicine, University of Montreal, Centre de Recherche du CHU Ste-Justine, Montreal, PQ, Canada H3T 1C5; Canada; E-Mail: email@example.com
Abstract: With the advent of high throughput DNA sequencing technologies, it has become feasible to determine the sequence of whole genomes. There are now large numbers of completed microbial genomes, sequenced essentially to completion, as well as significant numbers of metazoan species (animal – across multiple phyla, and plant) sequenced to near completion. In most cases, only one or a few representative genomes of each metazoan species have been sequenced, but further cost reductions make it likely that this will change in the near future. On the other hand, numerous individual human genomes have been sequenced, some of which data are fully accessible via public databases. The availability of such extensive collections of sequence data allows experimental studies of hitherto more theoretical questions in developmental and evolutionary biology. One such is the information content contained in genomes. This question is inextricably related to the concept of complexity in biological systems. This article will briefly review the literature on complexity and alternative ways to measure it, and will document attempts to apply such measures to genomes, but with a fresh viewpoint stimulated by the explosion of new experimental data.
Type of Paper: Review
Title: Recruitment of Transcription Complexes to Enhancers and the Role of Enhancer Transcription.
Authors: Jared Stees 1, Fred Varn 1, John Strouboulis 2 and Jörg Bungert 1
Affiliations: 1 Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville 32610, FL, USA; E-Mail: firstname.lastname@example.org
2 Institute of Molecular Oncology, BSRC Alexander Fleming, Varkiza, Greece; E-Mail: email@example.com
Abstract: Enhancer elements regulate the tissue-and developmental stage specific expression of genes. Recent estimates suggest that there are more than 50,000 enhancers in mammalian cells. At least a subset of enhancers has been shown to recruit RNA polymerase II transcription complexes and to generate enhancer transcripts. Here, we review the current literature on enhancer function and discuss how transcription of enhancers or enhancer generated transcripts could contribute to the regulation of gene expression during the differentiation of cells.
Last update: 21 June 2012