The University of Toledo

BPG NEWS & UPDATES

2012 GREAT LAKES BIOINFORMATICS CONFERENCE, May 15-17, 2012

The 2012 GLBIO will be held at the University of Michigan, Ann Arbor, MI, Michigan League Conference Center.   Call for oral presentations, abstracts, posters, opened on October 14, 2011. Registration for the Conference will begin on November 1, 2011.

 Please click on this link, http://www.iscb.org/glbio2012, for complete details about the Conference; deadline dates, accommodations, maps, airport and parking information, etc.  If you have questions or need assistance, please contact Jo Anne Gray, BPG Program Secretary, at 419-383-6883, or via email, joanne.gray@utoledo.edu.

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MAYO CLINIC PILOT STUDY:  Mayo Clinic plans to sequence patients' genomes to personalize care.
A new project at the Mayo Clinic will give doctors the genetic information they need to choose drugs that will work best and minimize side effects.

Click here for full article

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BIOINFORMATIC STUDENTS DEVELOP SOFTWARE

The students of Dr. Alexei Fedorov, Vice Director of the BPG Program, and director of the Bioinformatics lab, have their own software, which they developed themselves. Please click on the link below to view their photo and accomplishments:

http://bpg.utoledo.edu/~aprakash/fedorov_lab/

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Bioinformatics -related article in Nature: October 2011
"Inspiration for Informatics: Trainees in bioinformatics and computational biology should seek depth of knowledge over breadth." 

Please click here to view entire article.


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PUBLICATIONS AND PRESENTATIONS BY STUDENTS IN THE BPG PROGRAM (click on link to read complete article)

Shepard S, McSweeny A, Serpen G, Fedorov A. Exploiting mid-range DNA patterns for sequence classification: binary abstraction Markov models Nucleic Acids Research doi: 10.1093/nar/gks154, 2012.

Nabiyouni M, Prakash A., Fedorov A. Peculiarities in vertebrate codon bias suggest a highly GC-rich ancestral genome. Submitted, December 2011.

He J, Shepard S.S., Fedorov A., Leisner S. Identification of candidate genes regulated through argonaute4-dependent RNA-dependent DNA methylation in Arabidopsis. Under revision for Gene.

Shepard S, McSweeny A, Serpen G, Fedorov A. Binary-absrtacted Markov models and their application to sequence classification. Under minor review in Nucleic Acids Research, 2011.

Yu B, Fey P, Kestin-Pilcher KE, Fedorov A, Prakash A, Chisholm RL, Wu JY. Spliceosomal genes in the D. discoideum genome: a comparison with those in. sapiens, D. melanogaster, A. thaliana and S. cerevisiae. Protein Cell. May;2(5):395-409, 2011.

Prakash A, Bechtel J, Fedorov A. Genomic MRI – a public resource for studying sequence patterns within genomic DNA. J Vis Exp. 9;(51). pii: 2663, 2011

Rearick D, Prakash A, McSweeny A, Shepard S, Fedorova L, Fedorov A, Critical association of ncRNA with introns. Nucleic Acids Research, Nov. 2011, Vol. 39, No. 6, p. 2357-2366.

Presentation: Andrew McSweeny: "Biniary-abstraction Markov models and their application to sequence classification". Ohio Collaborative Conference in Bioinformatics (OCCBIO), June 15-17, 2010, The Ohio State University, Columbus, Ohio.

Bazeley P, Shepelev V, Talebizadeh Z, Butler M, Fedorova L, Filatov V, Fedorov A. snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. Gene, 2008, 408:172-179.

Bechtel J, Wittenschlaeger T, Dwyer T, Song J, Arunachalam S, Ramakrishnan SK, Shepard S, Fedorov A. Genomic mid-range inhomogeneity immpacts RNA secondary structures.  Genome Biology 2007 (submitted, MS ID 2023183612167122)

Shepard S., McCreary M., Fedorov A. “The peculiarities of large intron splicing in animals”, PLoS ONE, 2009, 4(11):e7853. 

Prakash A., Shepard S., Mileyeva-Biebesheimer O., He J., Hart B., Chen M., Amarachiniha S., Bechtel J., Fedorov A. “Molecular forces shaping human genomic sequence at mid-range scales”, BMC Genomics 2009, 10:513.

Bechtel J. M., Rajesh P., Ilikchyan I., Deng Y., Mishra P.K., Wang G., Wu X., Afonin K., Grose W., Wang Y., Khuder S., and Fedorov A. Calculation of Splicing Potential from the Alternative Splicing Mutation Database Research Notes 2008, 1:4.

24. Bechtel J. M., Rajesh P., Ilikchyan I., Deng Y., Mishra P.K., Wang G., Wu X., Afonin K., Grose W., Wang Y., Khuder S., and Fedorov A. The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence. Research Notes 2008, 1:3.

Havlioglu N., Wang J., Fushimi K., Vibranovski M.D., Kan Z., Gish W., Fedorov A., Long M., Wu J.Y. An intronic signal for alternative splicing in the human genome. PloS ONE 2007, 11:e1246.

Shepelev V., Fedorov A. Advances in the Exon-Intron Database. Briefings in Bioinformatics 2006, 7: 178-185.

19. Shao X., Shepelev V., Fedorov A. Bioinformatc analysis of exon repetition, exon scrambling and trans-splicing in humans. Bioinformatics 2006, 22:692-698.