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Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species

Manolis Kamvysselis, Nick Patterso, Bruce Birren, Bonnie Berger, Eric Lander
2003 Proceedings of the seventh annual international conference on Computational molecular biology - RECOMB '03  
In [13] we reported the genome sequences of S. paradoxus, S. mikatae and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae.  ...  In this companion paper we describe the mathematical and algorithmic results underpinning the analysis of these genomes.  ...  We thank Jon Butler, Sarah Calvo, Matt Endrizzi, James Galagan, David Jaffe, Joseph Lehar, Li-Jun Ma and all the people at the MIT/Whitehead Institute Center for Genome Research for their help and discussions  ... 
doi:10.1145/640075.640096 dblp:conf/recomb/KamvysselisPBBL03 fatcat:leok2fmzdzhk7ozhi6jejpgp5i

A Caenorhabditis motif compendium for studying transcriptional gene regulation

Christoph Dieterich, Ralf J Sommer
2008 BMC Genomics  
Description: We present an unbiased comparative approach to a regulatory motif compendium for Caenorhabditis species.  ...  This involves the assembly of a new nematode genome, whole genome alignments and assessment of conserved k-mers counts.  ...  Acknowledgements We thank Adrian Streit and Benjamin Schlager for valuable discussions. We also thank Michael Han for sharing a script to display multiple alignments.  ... 
doi:10.1186/1471-2164-9-30 pmid:18215260 pmcid:PMC2248174 fatcat:nwqd2typunccbi2guf2b5iair4

Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes

Lokesh Kumar, Andrew Breakspear, Corby Kistler, Li-Jun Ma, Xiaohui Xie
2010 BMC Genomics  
The conservation of regulatory pathways among the Fusarium genomes and the two yeast species reveals their functional significance, and provides new insights in their evolutionary importance among Ascomycete  ...  Conclusion: This study provides the first comprehensive list of candidate regulatory motifs in Fg, and underscores the power of comparative genomics in revealing functional elements among related genomes  ...  Acknowledgements We thank the Broad Institute for making the genomes of the three Fusarium species available before publication.  ... 
doi:10.1186/1471-2164-11-208 pmid:20346147 pmcid:PMC2853525 fatcat:a422cd3dt5do3p4qm6h6mlaf4m

MotifMap: integrative genome-wide maps of regulatory motif sites for model species

Kenneth Daily, Vishal R Patel, Paul Rigor, Xiaohui Xie, Pierre Baldi
2011 BMC Bioinformatics  
regulatory elements encoded in the genomes of model species.  ...  Results: The MotifMap system uses databases of transcription factor binding motifs, refined genome alignments, and a comparative genomic statistical approach to provide comprehensive maps of candidate  ...  for Genomics and Bioinformatics.  ... 
doi:10.1186/1471-2105-12-495 pmid:22208852 pmcid:PMC3293935 fatcat:iahpb3n64nhzrmiyqaxcl4zd5q

Discovery of regulatory elements in vertebrates through comparative genomics

Amol Prakash, Martin Tompa
2005 Nature Biotechnology  
E value of the enrichment in parentheses.  ...  The third column shows the number of genes of the cluster having any GO biological process annotation.  ...  ACKNOWLEDGMENTS We thank Mathieu Blanchette, Nan Li, Michal Linial, Larry Ruzzo, Saurabh Sinha, Zasha Weinberg, Zizhen Yao, the Ensembl Help Desk (in particular, Michael Schuster and Ewan Birney) and the  ... 
doi:10.1038/nbt1140 pmid:16211068 fatcat:ukxthkobqbdypplnd4j5lgwini

Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery

Manolis Kellis, Nick Patterson, Bruce Birren, Bonnie Berger, Eric S. Lander
2004 Journal of Computational Biology  
In Kellis et al. (2003) , we reported the genome sequences of S. paradoxus, S. mikatae, and S. bayanus and compared these three yeast species to their close relative, S. cerevisiae.  ...  The algorithms enabled the automatic identification of orthologs for more than 90% of genes and intergenic regions across the four species despite the large number of duplicated genes in the yeast genome  ...  Ideker, Sue Lindquist, and Owen Ozier in the Whitehead Institute for their help and discussions.  ... 
doi:10.1089/1066527041410319 pmid:15285895 fatcat:ah4hpydkbrh7lnop24o76wf62e

Sequencing and comparison of yeast species to identify genes and regulatory elements

Manolis Kellis, Nick Patterson, Matthew Endrizzi, Bruce Birren, Eric S. Lander
2003 Nature  
We investigated the conservation properties of known regulatory motifs and used the insights gained to design an approach for de novo discovery of regulatory motifs directly from the genome.  ...  The goal of this paper is to develop and apply general approaches for systematic analysis of protein-coding and regulatory elements within any genome by means of whole-genome comparisons with several related  ...  Correspondence and requests for materials should be addressed to M.K. (manoli@mit.edu) or E.S.L. (lander@wi.mit.edu).  ... 
doi:10.1038/nature01644 pmid:12748633 fatcat:icc3uzvybbacrmtnujtsk2div4

Fast, Sensitive Discovery of Conserved Genome-Wide Motifs

Nnamdi E. Ihuegbu, Gary D. Stormo, Jeremy Buhler
2012 Journal of Computational Biology  
We have developed Magma (Multiple Aligner of Genomic Multiple Alignments), a software tool for multiple species, multiple gene motif discovery.  ...  Magma identifies putative regulatory sites that are conserved across multiple species and occur near multiple genes throughout a reference genome.  ...  Funding was provided by NIH (grant HG00249 to G.D.S.) and NSF (grant ITR-427794 to J.B.).  ... 
doi:10.1089/cmb.2011.0249 pmid:22300316 pmcid:PMC3272693 fatcat:ttu5x7zhmbd2fbpegzqaploblq

Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

Xiaohui Xie, Jun Lu, E. J. Kulbokas, Todd R. Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric S. Lander, Manolis Kellis
2005 Nature  
Here, we present a comparative analysis of the human, mouse, rat and dog genomes to create a systematic catalogue of common regulatory motifs in promoters and 3 0 untranslated regions (3 0 UTRs).  ...  Comparative genomics provides a powerful approach for the systematic discovery of functional elements in the human genome 1-8 , by virtue of their evolutionary conservation across related species.  ...  O'Neill and A. Subramanian for advice and discussions. This work was supported in part by grants from the National Human Genome Research Institute.  ... 
doi:10.1038/nature03441 pmid:15735639 pmcid:PMC2923337 fatcat:rlezg3lhnjd3hda7wwu66n3nde

Multi-species sequence comparison: the next frontier in genome annotation

Inna Dubchak, Kelly Frazer
2003 Genome Biology  
Most current computational tools have been designed for pairwise comparisons, and efficient extension of these tools to multiple species will require knowledge of the ideal evolutionary distance to choose  ...  and the development of new algorithms for alignment, analysis of conservation, and visualization of results.  ...  ID was partially supported by the Programs for Genomic Applications grant from the NHLBI/NIH.  ... 
doi:10.1186/gb-2003-4-12-122 pmid:14659006 pmcid:PMC329408 fatcat:sttdlxf5cnbnfgyxufhxw5bema

A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks

Zhen Gao, Ruizhe Zhao, Jianhua Ruan
2012 Proceedings of the 2012 ACM Research in Applied Computation Symposium on - RACS '12  
Thus, it can be used for species where previous knowledge of cis-regulatory motifs is unknown and has the potential to discover new transcription factor binding sites.  ...  regulatory networks discovery models.  ...  Acknowledgements This work was supported by NSF grants IOS-0848135, IIS-1218201, NIH grants SC3GM086305, U54CA113001, G12MD007591 (Computational Systems Biology Core), and a UTSA Tenure-track Research  ... 
doi:10.1145/2401603.2401620 dblp:conf/racs/GaoZR12 fatcat:rmiuoxv4izhcvjsbdqsqehvsla

Identifying the conserved network of cis-regulatory sites of a eukaryotic genome

T. Wang, G. D. Stormo
2005 Proceedings of the National Academy of Sciences of the United States of America  
We report a computational approach for identifying conserved regulatory motifs of an organism directly from whole genome sequences of several related species without reliance on additional information.  ...  ͉ regulatory network Methods We developed a framework to identify conserved regulatory motifs and their networks from genome sequences of related species.  ...  T.W. was supported partially by National Institutes of Health Training Grant T32HG00045 and by a Kauffman Fellowship.  ... 
doi:10.1073/pnas.0505147102 pmid:16301543 pmcid:PMC1297658 fatcat:xp73twxuxrbxtjss4m37zjv4ta

Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics

J. Gertz
2005 Genome Research  
The method is effective in finding motifs de novo and for refining known regulatory motifs in Saccharomyces cerevisiae.  ...  To identify these sequences, we developed an algorithm that searches for short, conserved sequence motifs in the genomes of related species.  ...  Acknowledgments We thank Ting Wang and Gary Stormo for providing the Patser program and for helpful discussions, Jon Armstrong and Elaine Mardis for printing our microarrays, Stan Fields for providing  ... 
doi:10.1101/gr.3859605 pmid:16077013 pmcid:PMC1182227 fatcat:zb4thd73nrazbpy33i72zpqglq

Prediction, Annotation, and Analysis of Human Promoters

M.Q. ZHANG
2003 Cold Spring Harbor Symposia on Quantitative Biology  
Acknowledgements I would like to thank all (including previous) members of Zhang lab and my collaborators for contributing most of the data and the figures, many before publications.  ...  The new pipeline, taking advantage of cross-species comparisons, can automatically annotate multiple genomes in parallel on a Linux cluster (Figure. 1) and have been used to create the initial reference  ...  Although comparative genomics has proved to be promising for discovering cisregulatory regions (Pennacchio and Rubin 2001) , because different promoter evolves with different rate, multiple species would  ... 
doi:10.1101/sqb.2003.68.217 pmid:15338621 fatcat:cnnsldcc7jeirm6yg2gz6kcwwe

Abstracts

I. K. Jordan
2003 Briefings in Bioinformatics  
Briefings in Bioinformatics aims to provide working biologists with an awareness and understanding of the computational approaches available for research and discovery.  ...  Publications in the areas of gene regulation, molecular evolution and bioinformatics resources from the second quarter of 2003 (April-June) are reviewed here.  ...  This resulted in the discovery of 647 sequence patterns, which were collapsed into 42 degenerate regulatory motifs.  ... 
doi:10.1093/bib/4.3.283 fatcat:kcvyyjn5ffhttetr6mit7iqfbm
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