Zobrazeno 1 - 10 of 151 pro vyhledávání: '"Computational Biology/Sequence Motif Analysis"'
1
Genome Analysis Reveals Interplay between 5′UTR Introns and Nuclear mRNA Export for Secretory and Mitochondrial Genes
Autor: Can Cenik, Melissa J. Moore, Alexander F. Palazzo, Stefan P. Tarnawsky, Adnan Derti, Murat Tasan, Abdalla Akef, Frederick P. Roth, Hon Nian Chua, Hui Zhang
Publikováno v: PLoS Genetics
PLoS Genetics, Vol 7, Iss 4, p e1001366 (2011)
In higher eukaryotes, messenger RNAs (mRNAs) are exported from the nucleus to the cytoplasm via factors deposited near the 5′ end of the transcript during splicing. The signal sequence coding region (SSCR) can support an alternative mRNA export (AL
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bc779f3e8d0c501cc52dc8eaa4849aaa
http://europepmc.org/articles/PMC3077370
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2
Ratio-based analysis of differential mRNA processing and expression of a polyadenylation factor mutant pcfs4 using arabidopsis tiling microarray
Autor: Yingjia Shen, Denghui Xing, Xiaohui Wu, Jianti Zheng, Qingshun Quinn Li, Diana M. Kroll, Guoli Ji
Publikováno v: PLoS ONE, Vol 6, Iss 2, p e14719 (2011)
PLoS ONE
Background Alternative polyadenylation as a mechanism in gene expression regulation has been widely recognized in recent years. Arabidopsis polyadenylation factor PCFS4 was shown to function in leaf development and in flowering time control. The func
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9d9f1e12016139a762bdecec90cdcdb6
http://europepmc.org/articles/PMC3045369?pdf=render
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3
G = MAT: Linking Transcription Factor Expression and DNA Binding Data
Autor: Sven Laur, Konstantin Tretyakov, Jaak Vilo
Publikováno v: PLoS ONE
PLoS ONE, Vol 6, Iss 1, p e14559 (2011)
Transcription factors are proteins that bind to motifs on the DNA and thus affect gene expression regulation. The qualitative description of the corresponding processes is therefore important for a better understanding of essential biological mechani
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::27deab64d54dcf774df2c1e47cb5d1da
http://europepmc.org/articles/PMC3031503
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4
Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs
Autor: William H. Majoros, Uwe Ohler
Publikováno v: PLoS Computational Biology, Vol 6, Iss 12, p e1001037 (2010)
PLoS Computational Biology
The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species conservation for this task have
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6329606cf5a1d836982dc5865390f447
http://europepmc.org/articles/PMC3002982?pdf=render
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5
Large-scale discovery and characterization of protein regulatory motifs in eukaryotes
Autor: Saeed Tavazoie, Daniel S. Lieber, Olivier Elemento
Publikováno v: PLoS ONE, Vol 5, Iss 12, p e14444 (2010)
PLoS ONE
The increasing ability to generate large-scale, quantitative proteomic data has brought with it the challenge of analyzing such data to discover the sequence elements that underlie systems-level protein behavior. Here we show that short, linear prote
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::60a3fb71876cd78e5acc200b7582629f
http://europepmc.org/articles/PMC3012054?pdf=render
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6
A Novel HMM-Based Method for Detecting Enriched Transcription Factor Binding Sites Reveals RUNX3 as a Potential Target in Pancreatic Cancer Biology
Autor: Nir Yosef, Roded Sharan, Eytan Ruppin, Yoram Oron, Marvin C. Gershengorn, Liron Levkovitz
Publikováno v: PLoS ONE
PLoS ONE, Vol 5, Iss 12, p e14423 (2010)
Background: Pancreatic adenocarcinoma (PAC) is one of the most intractable malignancies. In order to search for potential new therapeutic targets, we relied on computational methods aimed at identifying transcription factor binding sites (TFBSs) over
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3bd042a544dd26af08318e1ed41dd2e9
http://europepmc.org/articles/PMC3008686
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7
Assessing computational methods of cis-regulatory module prediction
Autor: Thomas A. Down, Sarah A. Teichmann, Jing Su
Publikováno v: PLoS Computational Biology, Vol 6, Iss 12, p e1001020 (2010)
PLoS Computational Biology
Computational methods attempting to identify instances of cis-regulatory modules (CRMs) in the genome face a challenging problem of searching for potentially interacting transcription factor binding sites while knowledge of the specific interactions
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aea7f7eff9925a5b2888bf89a6a9eb0c
http://europepmc.org/articles/PMC2996316?pdf=render
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8
Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification
Autor: Morten Nielsen, José M. Delfino, Elin Teppa, Cristina Marino Buslje, Tomás Di Domenico
Publikováno v: PLoS Computational Biology, Vol 6, Iss 11, p e1000978 (2010)
PLoS Computational Biology
Buslje, C M, Teppa, E, Di Doménico, T, Delfino, J M & Nielsen, M 2010, ' Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification ', P L o S Computational Biology (Online), vol. 6, no. 11 . https://doi.org/10.1371/journal.pcbi.1000978
Scopus-Elsevier
Identification of catalytic residues (CR) is essential for the characterization of enzyme function. CR are, in general, conserved and located in the functional site of a protein in order to attain their function. However, many non-catalytic residues
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f3259373c836d5c8f01d79c0bf53d16e
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21079665/?tool=EBI
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9
Of Bits and Bugs — On the Use of Bioinformatics and a Bacterial Crystal Structure to Solve a Eukaryotic Repeat-Protein Structure
Autor: Almut Graebsch, Dirk Kostrewa, Johannes Söding, Dierk Niessing, Stéphane Roche
Publikováno v: PLoS ONE
PLoS One
PLoS ONE 5:e13402 (2010)
PLoS ONE, Vol 5, Iss 10, p e13402 (2010)
ResearcherID
Pur-α is a nucleic acid-binding protein involved in cell cycle control, transcription, and neuronal function. Initially no prediction of the three-dimensional structure of Pur-α was possible. However, recently we solved the X-ray structure of Pur-
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a4ff949ceb8a52cfeeb3d874f8833789
http://europepmc.org/articles/PMC2954813
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10
Library of disordered patterns in 3D protein structures
Autor: Oxana V. Galzitskaya, Eugeniya I. Furletova, Michail A. Roytberg, Natalya S. Bogatyreva, Michail Yu. Lobanov
Publikováno v: PLoS Computational Biology, Vol 6, Iss 10, p e1000958 (2010)
PLoS Computational Biology
Intrinsically disordered regions serve as molecular recognition elements, which play an important role in the control of many cellular processes and signaling pathways. It is useful to be able to predict positions of disordered regions in protein cha
Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d0f8f775ec02a19b005dfa150fcd7a85
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20976197/?tool=EBI
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