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Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis

Matthew A. Hibbs, Chad L. Myers, Curtis Huttenhower, David C. Hess, Kai Li, Amy A. Caudy, Olga G. Troyanskaya, Andrey Rzhetsky
2009 PLoS Computational Biology  
Here we analyze and explore the results of this study that are broadly applicable for computationalists applying gene function prediction techniques, including a new experimental comparison with 48 genes  ...  While this study focused on a specific functional area in yeast, many of these observations may be useful in the contexts of other processes and organisms.  ...  We also thank the members of the Troyanskaya, Caudy, Botstein, Kruglyak, and Dunham laboratories for useful discussions and advice. Author Contributions  ... 
doi:10.1371/journal.pcbi.1000322 pmid:19300515 pmcid:PMC2654405 fatcat:qtroeg4sezb6vkn32xg3yiznl4

The Potential of Text Mining in Data Integration and Network Biology for Plant Research: A Case Study on Arabidopsis

S. Van Landeghem, S. De Bodt, Z. J. Drebert, D. Inze, Y. Van de Peer
2013 The Plant Cell  
In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all  ...  Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases.  ...  S.V.L. processed the text mining data, designed the manual evaluation study, and interpreted the curated data. Z.J.D. performed the manual evaluation. S.D.B. processed the CORNET data sets.  ... 
doi:10.1105/tpc.112.108753 pmid:23532071 pmcid:PMC3634689 fatcat:qhddrgf2n5cfjmtp7lli67qgxa

Yeast Gene Function Prediction from Different Data Sources: An Empirical Comparison

Ying Liu
2011 The Open Bioinformatics Journal  
In this paper, we report a comparative study of yeast gene function prediction using different data sources, namely microarray data, phylogenetic data, literature text data, and a combination of these  ...  In this paper, each of the data sets (microarray, phylogenetic, text mining, and the combined data sets) was partitioned into ten subsets with both positive and negative genes spread as equally as possible  ... 
doi:10.2174/1875036201105010069 fatcat:l2p4usyih5dgfkau6uh32nqake

A Bioinformatical Approach to Study the Endosomal Sorting Complex Required for Transport (ESCRT) Machinery in Protozoan Parasites: The Entamoeba histolytica Case [chapter]

Israel Lopez-Reyes, Cecilia Banuelos, Abigail Betanzos, Esther Orozco
2011 Bioinformatics - Trends and Methodologies  
Over the past years, bioinformatical tools have been widely used for the prediction and study of protein biology.  ...  The Resource for Studying Biological Macromolecules curates and annotates the PDB data according to agreed upon standards and also provides a variety of tools and resources.  ...  This book suits young researchers who seek basic fundamentals of bioinformatic skills such as data mining, data integration, sequence analysis and gene expression analysis as well as scientists who are  ... 
doi:10.5772/19480 fatcat:7zojjgfc2va3jcg5ptnqlazn2q

Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study

Yongfei Wang, Shoukai Lin, Qi Song, Kuan Li, Huan Tao, Jian Huang, Xinhai Chen, Shufu Que, Huaqin He
2014 BMC Genomics  
Results: In this study, we combined orthology-based approach with expression association data to screen rice Hsps for the expression patterns of which strongly correlated with that of heat responsive probe-sets  ...  Then, using a combination of interolog and expression profile-based methods, we inferred 430 interactors of Hsp70s in rice, and validated the interactions by co-localization and function-based methods.  ...  Acknowledgements This work was supported by the Natural Science Foundation of China and Fujian (grant nos. 31270454, 61163047 and 2013J01077), a grant from the Education Department of Fujian (grant no.  ... 
doi:10.1186/1471-2164-15-344 pmid:24884676 pmcid:PMC4035072 fatcat:w43jd5p7wzbqjcc6dhix7b7ln4

Prediction of Protein–Protein Interactions by Evidence Combining Methods

Ji-Wei Chang, Yan-Qing Zhou, Muhammad Ul Qamar, Ling-Ling Chen, Yu-Duan Ding
2016 International Journal of Molecular Sciences  
topology and text mining.  ...  However, computational approaches for PPI predication supported by rapid accumulation of data generated from experimental techniques, 3D structure definitions, and genome sequencing have boosted the map  ...  Text Mining: Protein-protein interactions can also be predicted using text mining (TM).  ... 
doi:10.3390/ijms17111946 pmid:27879651 pmcid:PMC5133940 fatcat:kttovj6jsnhhhenyjmksj6wffa


2007 Journal of Bioinformatics and Computational Biology  
The need for further development of comprehensive systems biology techniques that can utilize the ever-increasing data presented by the genomics and proteomics communities is emphasized.  ...  Because they incorporate structural and experimental data that is not used in sequence-based methods, they can provide additional accuracy and reliability to protein function prediction.  ...  Acknowledgments This work is partially supported by National Institutes of Health (R01 GM075004 and U24 GM077905) and National Science Foundation (DMS 0604776).  ... 
doi:10.1142/s0219720007002503 pmid:17477489 fatcat:n7a5cf3hkbaivbyv6yyjm45wdq

CisMiner: Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining

Carmen Navarro, Francisco J. Lopez, Carlos Cano, Fernando Garcia-Alcalde, Armando Blanco, Leonardo Mariño-Ramírez
2014 PLoS ONE  
CisMiner can be queried for the results presented in this work and can also perform a customized cis-regulatory module prediction on a query set of transcription factor binding sites provided by the user  ...  Results obtained for a set of well-known binding sites in the S. cerevisiae genome show that our method yields highly reliable predictions.  ...  The same applies for approaches that use orthologous sequences to a certain gene or a set of co-regulated genes. These approaches are useful for the study of already known processes.  ... 
doi:10.1371/journal.pone.0108065 pmid:25268582 pmcid:PMC4182448 fatcat:gfhsgqb4hbcpdcl2vrx3gj5cwa

Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae

I. Williams
2004 Nucleic Acids Research  
A novel method analysing specific nucleotide combinations in the 3 0 context region revealed positions +1,2,3,5 and +1,2,3,6 after the stop codon were most predictive of termination efficiency.  ...  Downstream of yeast open reading frames (ORFs), further in-frame stop codons were significantly over-represented at the +1, +2 and +3 codon positions after the ORF, acting to limit readthrough.  ...  A data mining method for analysing 3 0 context data A new data mining method was employed to analyse the 3 0 context nucleotide frequencies (33) .  ... 
doi:10.1093/nar/gkh1004 pmid:15602002 pmcid:PMC545446 fatcat:twffqmaxzveorpfc4ddjfxktty

DextMP: deep dive into text for predicting moonlighting proteins

Ishita K Khan, Mansurul Bhuiyan, Daisuke Kihara
2017 Bioinformatics  
Lastly, we ran DextMP with the best performing language models and text-based feature combinations on three genomes, human, yeast and Xenopus laevis, and found that about 2.5-35% of the proteomes are potential  ...  Currently MPs are not labeled as such in biological databases even in cases where multiple distinct functions are known for the proteins.  ...  Acknowledgements The authors thank Sarah Rodenbeck for proofreading the manuscript. Funding This work was partly supported by the National Science Foundation (DBI1262189).  ... 
doi:10.1093/bioinformatics/btx231 pmid:28881966 pmcid:PMC5870774 fatcat:ljokqbym4bcrvhsd643xetev4q

Improving protein function prediction methods with integrated literature data

Aaron P Gabow, Sonia M Leach, William A Baumgartner, Lawrence E Hunter, Debra S Goldberg
2008 BMC Bioinformatics  
Though arguably biased toward known genes, co-occurrence data provides critical additional links to well-studied regions in the interaction network that graph-theoretic function prediction algorithms can  ...  Conclusion: Co-occurrence data is a valuable supplemental source for graph-theoretic function prediction algorithms.  ...  IEA assignments in GO for each organism.  ... 
doi:10.1186/1471-2105-9-198 pmid:18412966 pmcid:PMC2375131 fatcat:znbaabkhvfga7pi6bia6qhwxam

Interspecies data mining to predict novel ING-protein interactions in human

Paul MK Gordon, Mohamed A Soliman, Pinaki Bose, Quang Trinh, Christoph W Sensen, Karl Riabowol
2008 BMC Genomics  
Validation of our approach by traditional laboratory techniques shows that we can extract value from the voluminous weak interaction data already elucidated in yeast and fly databases.  ...  The bioinformatics approach we describe can be used to create an interaction prediction list for any human proteins with yeast homolog(s).  ...  Tanya Paull for Rad50, Steve Pellech and James Woodgett for p38MAPK and Richard Vaillancourt for MEKK4 DNA expression constructs.  ... 
doi:10.1186/1471-2164-9-426 pmid:18801192 pmcid:PMC2565686 fatcat:q5crxop7bnaepfdjo5h2zeec2y

Domain-mediated protein interaction prediction: From genome to network

Jüri Reimand, Shirley Hui, Shobhit Jain, Brian Law, Gary D. Bader
2012 FEBS Letters  
This review focuses on computational prediction and analysis of PRM-mediated networks and discusses sequence-and structure-based interaction predictors, techniques and datasets for identifying physiologically  ...  Solving the problem of predicting protein interactions from the genome sequence will lead to increased understanding of complex networks, evolution and human disease.  ...  Text mining Text mining, the technique of automated information extraction from literature, can also be used to predict PPIs.  ... 
doi:10.1016/j.febslet.2012.04.027 pmid:22561014 fatcat:z4tcqpaq6zgohnqizpnt5wjiam

A Multiobjective Evolutionary Conceptual Clustering Methodology for Gene Annotation Within Structural Databases: A Case of Study on the Gene Ontology Database

R.C. Romero-Zaliz, C. Rubio-Escudero, J.P. Cobb, F. Herrera, O. Cordon, I. Zwir
2008 IEEE Transactions on Evolutionary Computation  
The combination of evolutionary algorithms with multiobjective and multimodal optimization techniques constitutes a suitable tool for solving this problem.  ...  These models can explain and predict phenotypes in the immunoinflammatory response problem, similar to those provided by gene expression or other genetic markers.  ...  Huang, and A. Polpitiya for useful suggestions.  ... 
doi:10.1109/tevc.2008.915995 fatcat:dbgsmopsgfbknprjhcpf43u47a

Prediction of Regulatory Elements [chapter]

Albin Sandelin
2008 Msphere  
Experimental efforts towards understanding the regulation of genes is laborious and expensive, but can be substantially accelerated with the use of computational predictions.  ...  one of the most fundamental processes for all life forms, transcriptional regulation remains an intriguing and challenging subject for biomedical research.  ...  In a case study, we showed that nuclear receptor genes have a high potential for cross-or auto regulation using the pufferfish genome as a predictive platform.  ... 
doi:10.1007/978-1-60327-429-6_11 pmid:18712306 fatcat:ku3wqjcnmjaw5ncqdaszcpzpj4
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