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Gene teams with relaxed proximity constraint

S. Kim, J.-H. Choi, J. Yang
2005 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05)  
In this paper, we generalized the gene team model, that looks for gene clusters in a physically clustered form, to multiple genome cases with relaxed constraint.  ...  Physical proximity among genes, known as gene team, is a very useful concept to discover functionally related genes in multiple genomes.  ...  Acknowledgment This work is partially supported by INGEN (Indiana Genomics Initiatives) and NSF DBI-0237901. Thanks also to the two anonymous reviewers for their comments.  ... 
doi:10.1109/csb.2005.33 dblp:conf/csb/KimCY05 fatcat:afvnzlexpnbmzf6k2x7d2yfsby

ALIGNSCOPE: A VISUAL MINING TOOL FOR GENE TEAM FINDING WITH WHOLE GENOME ALIGNMENT

HEE-JEONG JIN, HYE-JUNG KIM, JEONG-HYEON CHOI, HWAN-GUE CHO
2005 Proceedings of the 4th Asia-Pacific Bioinformatics Conference  
In this paper, we propose a method for identifying and visualizing the alignment of the whole genome alignment, especially for detecting gene clusters between two aligned genomes.  ...  Recently identifying sets of orthologous genes in several genomes has become getting important, since a cluster of similar genes helps us to predict the function of unknown genes.  ...  We gratefully credit the thoughtful reviewers, who provided substantial constructive criticism on an earlier version of this note.  ... 
doi:10.1142/9781860947292_0010 fatcat:vqvcwgbjazhedjmjznp6yvukoy

Bidirectional best hit r-window gene clusters

Melvin Zhang, Hon Wai Leong
2010 BMC Bioinformatics  
Conserved gene clusters are groups of genes that are located close to one another in the genomes of several species. They tend to code for proteins that have a functional interaction.  ...  The identification of conserved gene clusters is an important step towards understanding genome evolution and predicting gene function.  ...  Acknowledgements We would like to thank Wing-Kin Sung from the National University of Singapore for initiating discussions on algorithmic improvements to our algorithm and the anonymous reviewers for providing  ... 
doi:10.1186/1471-2105-11-s1-s63 pmid:20122239 pmcid:PMC3009537 fatcat:ldpobkhsa5fzraetjvdbanqyfe

The Incompatible Desiderata of Gene Cluster Properties [chapter]

Rose Hoberman, Dannie Durand
2005 Lecture Notes in Computer Science  
We formalize and analyze the desirable properties of gene clusters and cluster definitions.  ...  There is widespread interest in comparative genomics in determining if historically and/or functionally related genes are spatially clustered in the genome, and whether the same sets of genes reappear  ...  Raghupathy for comments on the manuscript, and David Sankoff for helpful discussion and for suggesting the title of the paper.  ... 
doi:10.1007/11554714_7 fatcat:sk5rozxlz5bp3apulohama5oxi

Analysis of Gene Order Evolution Beyond Single-Copy Genes [chapter]

Nadia El-Mabrouk, David Sankoff
2012 Msphere  
The purpose of this chapter is to provide a comprehensive review of the field of genome rearrangement, i.e., comparative genomics based on representation of genomes as ordered sequences of signed genes  ...  We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely  ...  A first formal model for max-gap clusters in permutations was introduced in [9] under the name of gene team, and algorithmic and statistical properties discussed in [66] .  ... 
doi:10.1007/978-1-61779-582-4_15 pmid:22407718 fatcat:kerbedfsgrgi5npicdlbd6u4aa

Gene Cluster Statistics with Gene Families

N. Raghupathy, D. Durand
2009 Molecular biology and evolution  
Demonstrating the statistical significance of such "gene clusters" is an essential component of comparative genomic analyses.  ...  Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes.  ...  Chebolu and A. Frieze for helpful discussions and A. Goldman, R. Hoberman, N. Song, B. Vernot, R. Sedgewick, and J. Joseph for their help in performing the simulation experiments.  ... 
doi:10.1093/molbev/msp002 pmid:19150803 pmcid:PMC2668827 fatcat:jd52wyg4ffaflh3zu76juy3qga

Identification of genomic features using microsyntenies of domains: Domain teams

S. Pasek
2005 Genome Research  
Here, we want to process realistic models of chromosomes, in which genes (or genomic segments of several genes) can be duplicated within a chromosome, or be absent from some other chromosome(s).  ...  The automated and fast detection of domain teams, together with its increased sensitivity at identifying segments of identical (protein-coding) gene contents as well as gene fusions, should prove a useful  ...  Acknowledgments We thank the Infobiogen team for their patience and understanding during very long runs and M. Marshall from the Pfam team for her help in retrieving the proper annotation files.  ... 
doi:10.1101/gr.3638405 pmid:15899966 pmcid:PMC1142477 fatcat:qcs6txe6yrazrocf53b7ja6nzy

Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions

Chaoyue Liu, Benjamin Wright, Emma Allen-Vercoe, Hong Gu, Robert Beiko, Tal Dagan
2018 Genome Biology and Evolution  
We propose a new approach that uses a coevolutionary method defined by Pagel to account for the phylogenetic relationships amongst target organisms, and a hierarchical-clustering approach to define sets  ...  Homologous genes in prokaryotes can be described using phylogenetic profiles which summarize their patterns of presence or absence across a set of genomes.  ...  We thank the members of the Broad Institute's Genome Sequencing, Assembly and Annotation Teams, including Sarah Young, Peg Priest, and Qiandong Zeng.  ... 
doi:10.1093/gbe/evy178 pmid:30137329 fatcat:up4m4sxyuvgu3a2zhyk3zvhoga

A gene pattern mining algorithm using interchangeable gene sets for prokaryotes

Meng Hu, Kwangmin Choi, Wei Su, Sun Kim, Jiong Yang
2008 BMC Bioinformatics  
There are several well developed algorithms for predicting gene patterns in a pair of genomes, such as FISH and DAGchainer.  ...  Results: In this paper, we propose a novel algorithm for mining gene patterns in more than two prokaryote genomes using interchangeable sets.  ...  Acknowledgement Kim was partially supported by a Career Award DBI-0237901 from National Science Foundation USA. Yang was partially supported by a grant from NSF (CNS-0551693).  ... 
doi:10.1186/1471-2105-9-124 pmid:18302784 pmcid:PMC2279103 fatcat:yvps6w4ysrdj3boxxnlcdx7idm

Identifying Conserved Gene Clusters in the Presence of Homology Families

Xin He, Michael H. Goldwasser
2005 Journal of Computational Biology  
In this paper, we present a new model and algorithm for identifying conserved gene clusters from pairwise genome comparison. This generalizes a recent model called "gene teams".  ...  The study of conserved gene clusters is important for understanding the forces behind genome organization and evolution, as well as the function of individual genes or gene groups.  ...  The authors are grateful to Howard Laten and Bryan Picket for helpful conversations, to Mathieu Raffinot for helpful comments, and to the anonymous referees for increasing our awareness of the issues raised  ... 
doi:10.1089/cmb.2005.12.638 pmid:16108708 fatcat:nceoatwcafhxnacm67kvsbxs5e

Identifying conserved gene clusters in the presence of orthologous groups

Xin He, Michael H. Goldwasser
2004 Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04  
In this paper, we present a new model and algorithm for identifying conserved gene clusters from pairwise genome comparison. This generalizes a recent model called "gene teams."  ...  A gene team is a set of orthologous genes that appear in two or more species, possibly in a different order yet with the distance of adjacent genes in the team for each chromosome always no more than a  ...  RELATED WORK Various computational methods have been proposed to identify conserved gene clusters by comparison of multiple genomes, both experimentally and formally.  ... 
doi:10.1145/974614.974650 dblp:conf/recomb/HeG04 fatcat:imit73skezez5eazqtmjnwcme4

Phylogenetic tree inference from local gene content [article]

Galina Glazko, Michael Gensheimer, Arcady Mushegian
2015 bioRxiv   pre-print
Results: We expand the repertoire of genome-wide traits available for phylogeny building, by developing a practical approach for measuring local gene conservation in two genomes.  ...  Background: Complete genome sequences provide many new characters suitable for studying phylogenetic relationships.  ...  When our work was in progress, Gene Teams, a rigorous formalization for the concept of "closely placed genes" on two chromosomes, was suggested [26] .  ... 
doi:10.1101/017699 fatcat:r272t4br2nfgnlprqusj2hixgy

Travelling the world of gene-gene interactions

K. Van Steen
2011 Briefings in Bioinformatics  
The search for epistasis or gene^gene interaction effects on traits of interest is marked by an exponential growth, not only in terms of methodological development, but also in terms of practical applications  ...  gene^gene interaction analysis.  ...  [181] used functional genetic networks or a map of biological interactions between genes to reduce to increase the power to test for the existence of gene-gene interactions throughout the genome.  ... 
doi:10.1093/bib/bbr012 pmid:21441561 fatcat:3kojyhlvfrgjrjbjtrovmg2aaa

GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data

Tizian Schulz, Jens Stoye, Daniel Doerr
2018 BMC Genomics  
We use data obtained from Hi-C experiments to provide new evidence for the existence of spatial gene clusters.  ...  Our model generalizes a popular computational model for gene cluster prediction, called δ-teams, from sequences to graphs.  ...  About this supplement This article has been published as part of BMC Genomics Volume 19 Supplement 5, 2018: Proceedings of the 15th Annual Research in Computational Molecular Biology (RECOMB) Comparative  ... 
doi:10.1186/s12864-018-4622-0 pmid:29745835 pmcid:PMC5998887 fatcat:loguxosqznbv3luvturpf56dhy

Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation

Michael S Werner, Bogdan Sieriebriennikov, Neel Prabh, Tobias Loschko, Christa Lanz, Ralf J Sommer
2018 Genome Research  
Acknowledgments We thank current members of the Sommer laboratory and Dr. Talia Karasov for thoughtful critique of experiments, results, and interpretations.  ...  This genome-wide perspective also supports the model that location into open chromatin is a critical factor for origination, or at least transcription, of new genes.  ...  Thus, although recombination in the arms appears to be a furnace for new gene generation, most of these genes are repressed (expression groups 3 and 4) and have a higher barrier for functionalization.  ... 
doi:10.1101/gr.234872.118 pmid:30232198 pmcid:PMC6211652 fatcat:2xhitvalcfafrnb7ddzp3rqtly
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